Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase.

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithm to reconstruct structural information from single-particle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core.

Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)3]2+ complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystal structure for the residues at the protein interface is ∼1.4 Å. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.

Evolutionarily Conserved Allosteric Communication in Protein Tyrosine Phosphatases.

Protein tyrosine phosphatases (PTPs) are an important class of regulatory enzymes that exhibit aberrant activities in a wide range of diseases. A detailed mapping of allosteric communication in these enzymes could, thus, reveal the structural basis of physiologically relevant-and, perhaps, therapeutically informative-perturbations (i.e., mutations, post-translational modifications, or binding events) that influence their catalytic states. This study combines detailed biophysical studies of protein tyrosine phosphatase 1B (PTP1B) with bioinformatic analyses of the PTP family to examine allosteric communication in this class of enzymes. Results of X-ray crystallography, molecular dynamics simulations, and sequence-based statistical analyses indicate that PTP1B possesses a broadly distributed allosteric network that is evolutionarily conserved across the PTP family, and findings from both kinetic studies and mutational analyses show that this network is functionally intact in sequence-diverse PTPs. The allosteric network resolved in this study reveals new sites for targeting allosteric inhibitors of PTPs and helps explain the functional influence of a diverse set of disease-associated mutations.

Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation.

Protein tyrosine phosphatases (PTPs) contribute to a striking variety of human diseases, yet they remain vexingly difficult to inhibit with uncharged, cell-permeable molecules; no inhibitors of PTPs have been approved for clinical use. This study uses a broad set of biophysical analyses to evaluate the use of abietane-type diterpenoids, a biologically active class of phytometabolites with largely nonpolar structures, for the development of pharmaceutically relevant PTP inhibitors. Results of nuclear magnetic resonance analyses, mutational studies, and molecular dynamics simulations indicate that abietic acid can inhibit protein tyrosine phosphatase 1B, a negative regulator of insulin signaling and an elusive drug target, by binding to its active site in a non-substrate-like manner that stabilizes the catalytically essential WPD loop in an inactive conformation; detailed kinetic studies, in turn, show that minor changes in the structures of abietane-type diterpenoids (e.g., the addition of hydrogens) can improve potency (i.e., lower IC50) by 7-fold. These findings elucidate a previously uncharacterized mechanism of diterpenoid-mediated inhibition and suggest, more broadly, that abietane-type diterpenoids are a promising source of structurally diverse-and, intriguingly, microbially synthesizable-molecules on which to base the design of new PTP-inhibiting therapeutics.

Xi-cam: a versatile interface for data visualization and analysis.

Xi-cam is an extensible platform for data management, analysis and visualization. Xi-cam aims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core of Xi-cam is an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. With Xi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data. Xi-cam's plugin-based architecture targets cross-facility and cross-technique collaborative development, in support of multi-modal analysis. Xi-cam is open-source and cross-platform, and available for download on GitHub.

Iterative phasing for fluctuation X-ray scattering.

Fluctuation X-ray scattering (FXS) is an extension of small- and wide-angle X-ray scattering in which the X-ray snapshots are taken below rotational diffusion times. This technique, performed using a free electron laser or ultrabright synchrotron source, provides significantly more experimental information compared with traditional solution scattering methods. We develop a multitiered iterative phasing algorithm to determine the underlying structure of the scattering object from FXS data.

Immune Cell Induced Migration of Osteoprogenitor Cells Is Mediated by TGF-ß Dependent Upregulation of NOX4 and Activation of Focal Adhesion Kinase.

The cytokines secreted by immune cells have a large impact on the tissue, surrounding a fracture, e.g., by attraction of osteoprogenitor cells. However, the underlying mechanisms are not yet fully understood. Thus, this study aims at investigating molecular mechanisms of the immune cell-mediated migration of immature primary human osteoblasts (phOBs), with transforming growth factor beta (TGF-ß), nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 4 (NOX4) and focal adhesion kinase (FAK) as possible regulators. Monocyte- and macrophage (THP-1 cells ± phorbol 12-myristate 13-acetate (PMA) treatment)-conditioned media, other than the granulocyte-conditioned medium (HL-60 cells + dimethyl sulfoxide (DMSO) treatment), induce migration of phOBs. Monocyte- and macrophage (THP-1 cells)-conditioned media activate Smad3-dependent TGF-ß signaling in the phOBs. Stimulation with TGF-ß promotes migration of phOBs. Furthermore, TGF-ß treatment strongly induces NOX4 expression on both mRNA and protein levels. The associated reactive oxygen species (ROS) accumulation results in phosphorylation (Y397) of FAK. Blocking TGF-ß signaling, NOX4 activity and FAK signaling effectively inhibits the migration of phOBs towards TGF-ß. In summary, our data suggest that monocytic- and macrophage-like cells induce migration of phOBs in a TGF-ß-dependent manner, with TGF-ß-dependent induction of NOX4, associated production of ROS and resulting activation of FAK as key mediators.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses.

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle.

Virus-like particles are used to encapsulate drugs, imaging agents, enzymes, and other biologically active molecules in order to enhance their function. However, the size of most virus-like particles is inflexible, precluding the design of appropriately sized containers for different applications. Here, we describe a chromatographic selection for virus-like particle assembly. Using this selection, we identified a single amino acid substitution to the coat protein of bacteriophage MS2 that mediates a uniform switch in particle geometry from T = 3 to T = 1 icosahedral symmetry. The resulting smaller particle retains the ability to be disassembled and reassembled in vitro and to be chemically modified to load cargo into its interior cavity. The pair of 27 and 17 nm MS2 particles will allow direct examination of the effect of size on function in established applications of virus-like particles, including drug delivery and imaging.

Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase.

This study uses mutants of human carbonic anhydrase (HCAII) to examine how changes in the organization of water within a binding pocket can alter the thermodynamics of protein-ligand association. Results from calorimetric, crystallographic, and theoretical analyses suggest that most mutations strengthen networks of water-mediated hydrogen bonds and reduce binding affinity by increasing the enthalpic cost and, to a lesser extent, the entropic benefit of rearranging those networks during binding. The organization of water within a binding pocket can thus determine whether the hydrophobic interactions in which it engages are enthalpy-driven or entropy-driven. Our findings highlight a possible asymmetry in protein-ligand association by suggesting that, within the confines of the binding pocket of HCAII, binding events associated with enthalpically favorable rearrangements of water are stronger than those associated with entropically favorable ones.

Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine ß-Lactamases by Relieving Steric Strain.

Serine ß-lactamases are bacterial enzymes that hydrolyze ß-lactam antibiotics. They utilize an active-site serine residue as a nucleophile, forming an acyl-enzyme intermediate during hydrolysis. In this study, thermal denaturation experiments as well as X-ray crystallography were performed to test the effect of substitution of the catalytic serine with glycine on protein stability in serine ß-lactamases. Six different enzymes comprising representatives from each of the three classes of serine ß-lactamases were examined, including TEM-1, CTX-M-14, and KPC-2 of class A, P99 of class C, and OXA-48 and OXA-163 of class D. For each enzyme, the wild type and a serine-to-glycine mutant were evaluated for stability. The glycine mutants all exhibited enhanced thermostability compared to that of the wild type. In contrast, alanine substitutions of the catalytic serine in TEM-1, OXA-48, and OXA-163 did not alter stability, suggesting removal of the Cß atom is key to the stability increase associated with the glycine mutants. The X-ray crystal structures of P99 S64G, OXA-48 S70G and S70A, and OXA-163 S70G suggest that removal of the side chain of the catalytic serine releases steric strain to improve enzyme stability. Additionally, analysis of the torsion angles at the nucleophile position indicates that the glycine mutants exhibit improved distance and angular parameters of the intrahelical hydrogen bond network compared to those of the wild-type enzymes, which is also consistent with increased stability. The increased stability of the mutants indicates that the enzyme pays a price in stability for the presence of a side chain at the catalytic serine position but that the cost is necessary in that removal of the serine drastically impairs function. These findings support the stability-function hypothesis, which states that active-site residues are optimized for substrate binding and catalysis but that the requirements for catalysis are often not consistent with the requirements for optimal stability.

Computer-assisted navigation is beneficial both in primary and revision surgery with modular rotating-hinge knee arthroplasty.

PURPOSE: The objective of the present study was to explore the effect of navigation on the reconstruction of the mechanical leg axis, implant positioning and the restoration of the joint line in hinged knee arthroplasty in vivo. We present the first 1- to 3-year clinical and radiological results following computer-navigated implantation of the EnduRo modular rotating-hinge knee arthroplasty system (Aesculap AG, Tuttlingen, Germany) as a primary or revision implant. METHODS: Thirty-one patients were analysed retrospectively. Indication was revision surgery in 18 patients and complex primary surgery in 13. The clinical and radiological results of 31 patients with a minimum follow-up of 12 months (mean 22.2 ± 6.2 months) were recorded. Age at follow-up was 55.2 ± 9.9 years. RESULTS: The absolute varus-valgus deviation from the neutral mechanical leg axis was determined at 5.1° ± 5.1° preoperatively and 2.1° ± 1.4° postoperatively. No intraoperative complications or problems with the navigation system were observed. At latest follow-up, no component loosening was detected. Based on the Knee Society Score, a knee score of 64.9 ± 17.7 points and a function score of 67.2 ± 27.3 points were achieved. CONCLUSIONS: Encouraging short-term clinical and radiological results with the computer-navigated implantation of the modular rotating-hinge EnduRo knee arthroplasty system were found in both primary and revision surgery. The navigation facilitated the reconstruction of the leg axis, implant positioning and the restoration of the joint line. LEVEL OF EVIDENCE: IV.

Structures of cGMP-Dependent Protein Kinase (PKG) Iα Leucine Zippers Reveal an Interchain Disulfide Bond Important for Dimer Stability.

cGMP-dependent protein kinase (PKG) Iα is a central regulator of smooth muscle tone and vasorelaxation. The N-terminal leucine zipper (LZ) domain dimerizes and targets PKG Iα by interacting with G-kinase-anchoring proteins. The PKG Iα LZ contains C42 that is known to form a disulfide bond upon oxidation and to activate PKG Iα. To understand the molecular details of the PKG Iα LZ and C42-C42' disulfide bond, we determined crystal structures of the PKG Iα wild-type (WT) LZ and C42L LZ. Our data demonstrate that the C42-C42' disulfide bond dramatically stabilizes PKG Iα and that the C42L mutant mimics the oxidized WT LZ structurally.

Long-term results using the straight tapered femoral cementless hip stem in total hip arthroplasty: a minimum of twenty-year follow-up.

We report the first long-term results of a prospective cohort study after total hip arthroplasty using the cementless Bicontact hip stem. Between 1987 and 1990, 250 total hip arthroplasties in 236 patients were performed using the cementless Bicontact hip stem. The average follow-up was 22.8 years (20.4-24.8) and average age at index surgery was 58.1 years. Eighty-one patients died and 9 were lost to follow-up. We noted 11 stem revisions revealing an overall Kaplan Meier survival rate of 95.0% (CI 95%: 91.1-97.2%). The average Harris Hip Score revealed 81 points (range 24-93). The Bicontact hip stem demonstrated high survival rates despite high ages and osteopenic changes, which are equivalent to other long-term reports of cementless stem fixation.

Long-term, non-invasive FTIR detection of low-dose ionizing radiation exposure.

Non-invasive methods of detecting radiation exposure show promise to improve upon current approaches to biological dosimetry in ease, speed, and accuracy. Here we developed a pipeline that employs Fourier transform infrared (FTIR) spectroscopy in the mid-infrared spectrum to identify a signature of low dose ionizing radiation exposure in mouse ear pinnae over time. Mice exposed to 0.1 to 2 Gy total body irradiation were repeatedly measured by FTIR at the stratum corneum of the ear pinnae. We found significant discriminative power for all doses and time-points out to 90 days after exposure. Classification accuracy was maximized when testing 14 days after exposure (specificity > 0.9 with a sensitivity threshold of 0.9) and dropped by roughly 30% sensitivity at 90 days. Infrared frequencies point towards biological changes in DNA conformation, lipid oxidation and accumulation and shifts in protein secondary structure. Since only hundreds of samples were used to learn the highly discriminative signature, developing human-relevant diagnostic capabilities is likely feasible and this non-invasive procedure points toward rapid, non-invasive, and reagent-free biodosimetry applications at population scales.

Component particle structure in heterogeneous disordered ensembles extracted from high-throughput fluctuation x-ray scattering.

The ring angular correlation function is a characteristic feature determined by the particle structure. Averaging over a large number of ring angular correlation functions calculated from x-ray diffraction patterns will cancel out the cross correlations between different particles and converge to the autocorrelation functions of single particles. Applied on heterogeneous disordered ensembles, the retrieved function is a linear combination of a single-particle autocorrelation function multiplied by the molar ratios in a heterogeneous system. Using this relation, the ring angular correlation functions of the individual component particles in the heterogeneous system can be retrieved through the high throughput fluctuation x-ray scattering technique. This method is demonstrated with a simulated heterogeneous system composed of nanorods, nanoprism, and nanorice.

Structure determination of LpxD from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.

Acinetobacter baumannii is a Gram-negative bacterium that is resistant to many currently available antibiotics. The protein LpxD is a component of the biosynthetic pathway for lipopolysaccharides in the outer membrane of this bacterium and is a potential target for new antibacterial agents. This paper describes the structure determination of apo forms of LpxD in space groups P2(1) and P4(3)22. These crystals contained six and three copies of the protein molecule in the asymmetric unit and diffracted to 2.8 and 2.7 Šresolution, respectively. A comparison of the multiple protein copies in the asymmetric units of these crystals reveals a common protein conformation and a conformation in which the relative orientation between the two major domains in the protein is altered.

Determining pair distance distribution function from SAXS data using parametric functionals.

Small angle X-ray scattering (SAXS) experiments are widely applied in structural biology. The SAXS experiments yield one-dimensional profile that needs further analysis to reveal structural information. The pair distance distribution function (PDDF), P(r), can provide molecular structures more intuitively, and it can be used to guide ab initio model reconstructions, making it a critical step to derive P(r) from experimental SAXS profiles. To calculate the P(r) curves, a new method based on a specially designed parametric functional form is developed, and implemented in pregxs. This method is tested against both synthetic and experimental data, the estimated P(r) functions are in good agreement with correct or known P(r). The method can also predict the molecular size. In summary, the pregxs method is robust and accurate in P(r) determination from SAXS profiles. The pregxs source code and an online server are available at http://www.sastbx.als.lbl.gov.

Analysis of the binding forces driving the tight interactions between beta-lactamase inhibitory protein-II (BLIP-II) and class A beta-lactamases.

ß-Lactamases hydrolyze ß-lactam antibiotics to provide drug resistance to bacteria. ß-Lactamase inhibitory protein-II (BLIP-II) is a potent proteinaceous inhibitor that exhibits low picomolar affinity for class A ß-lactamases. This study examines the driving forces for binding between BLIP-II and ß-lactamases using a combination of presteady state kinetics, isothermal titration calorimetry, and x-ray crystallography. The measured dissociation rate constants for BLIP-II and various ß-lactamases ranged from 10(-4) to 10(-7) s(-1) and are comparable with those found in some of the tightest known protein-protein interactions. The crystal structures of BLIP-II alone and in complex with Bacillus anthracis Bla1 ß-lactamase revealed no significant side-chain movement in BLIP-II in the complex versus the monomer. The structural rigidity of BLIP-II minimizes the loss of the entropy upon complex formation and, as indicated by thermodynamics experiments, may be a key determinant of the observed potent inhibition of ß-lactamases.