Wavelets filtering for classification of very noisy electron microscopic single particles images- application on structure determination of VP5-VP19C recombinant

BACKGROUND: Images of frozen hydrated [vitrified] virus particles were taken close-to-focus in an electron microscope containing structural signals at high spatial frequencies. These images had very low contrast due to the high levels of noise present in the image. The low contrast made particle selection, classification and orientation determination very difficult. The final purpose of the classification is to improve the signal-to-noise ratio of the particle representing the class, which is usually the average. In this paper, the proposed method is based on wavelet filtering and multi-resolution processing for the classification and reconstruction of this very noisy data. A multivariate statistical analysis (MSA) is used for this classification. RESULTS: The MSA classification method is noise dependant. A set of 2600 projections from a 3D map of a herpes simplex virus -to which noise was added- was classified by MSA. The classification shows the power of wavelet filtering in enhancing the quality of class averages (used in 3D reconstruction) compared to Fourier band pass filtering. A 3D reconstruction of a recombinant virus (VP5-VP19C) is presented as an application of multi-resolution processing for classification and reconstruction. CONCLUSION: The wavelet filtering and multi-resolution processing method proposed in this paper offers a new way for processing very noisy images obtained from electron cryo-microscopes. The multi-resolution and filtering improves the speed and accuracy of classification, which is vital for the 3D reconstruction of biological objects. The VP5-VP19C recombinant virus reconstruction presented here is an example, which demonstrates the power of this method. Without this processing, it is not possible to get the correct 3D map of this virus

Automatic particle detection in digitized electron micrographs

High resolution structural analysis of biological complexes can be carried out by single particle electron microscopy where a large number of particle images are available. Many approaches to automate the process of selection of particle positions from digitized electron micrograph images have been described, but so far none has proved as good as manual selection. This thesis describes a method which I have developed to locate such biological complexes by matching small boxed areas to a set of reference images using the radius of gyration, complemented by a series of other simple criteria. From the reference images, parameters such as the ratio between the average density of the central area and that in its surrounding band, and the density sum and variance are calculated. They are compared with corresponding values from a moving square window of densities extracted from the micrograph, and the coordinates of successfully matched candidate squares are recorded. Since the same particle is detected in a series of overlapping windows, candidates found to be within close proximity are grouped, and the best-fitting one is selected from each cluster. Along with a small stack of boxed reference images, a few specified parameter values, such as the particle radius and the minimum acceptable distance between particle centres are required to select the windows. Micrograph labels and other areas that do not contain appropriate specimens are automatically ignored in order to minimize false positives, and reduce the computing time. A computer program SLEUTH written to carry out this method of automatic particle detection includes a graphical user interface to assist the user in setting up the parameter values. The program has been tested successfully on a variety of different biological structures, from both negatively stained and ice-embedded specimens

X-ray and neutron scattering studies on some nanoscale structures in molecular biology

Scattering of X-rays and neutrons has been applied to the study of nanostructures with interesting biological functions. The systems studied were the protein calmodulin and its complexes, bacterial virus bacteriophage phi6, and the photosynthetic antenna complex from green sulfur bacteria, chlorosome. Information gathered using various structure determination methods has been combined to the low resolution information obtained from solution scattering. Conformational changes in calmodulin-ligand complex were studied by combining the directional information obtained from residual dipole couplings in nuclear magnetic resonance to the size information obtained from small-angle X-ray scattering from solution. The locations of non-structural protein components in a model of bacteriophage phi6, based mainly on electron microscopy, were determined by neutron scattering, deuterium labeling and contrast variation. New data are presented on the structure of the photosynthetic antenna complex of green sulfur bacteria and filamentous anoxygenic phototrophs, also known as the chlorosome. The X-ray scattering and electron cryomicroscopy results from this system are interpreted in the context of a new structural model detailed in the third paper of this dissertation. The model is found to be consistent with the results obtained from various chlorosome containing bacteria. The effect of carotenoid synthesis on the chlorosome structure and self-assembly are studied by carotenoid extraction, biosynthesis inhibition and genetic manipulation of the enzymes involved in carotenoid biosynthesis. Carotenoid composition and content are found to have a marked effect on the structural parameters and morphology of chlorosomes.Työssä on käytetty röntgen- ja neutronisäteilyn sirontaa molekyylibiologian kannalta mielenkiintoisten, nanometrin kokoluokkaan kuuluvien rakenteiden tutkimiseen. Tutkitut systeemit ovat proteiineja, proteiinikomplekseja, viruksia ja vihreiden bakteerien fotosynteesin kannalta tärkeä antennikompleksi, klorosomi. Erilaisten rakennetutkimusmenetelmien antamaa informaatiota on yhdistetty sirontamenetelmillä saatavaan matalan resoluution rakennetietoon. Ensimmäisessä osajulkaisussa proteiinin konformaatiomuutosta tutkittiin yhdistämällä ydinmagneettisen resonanssin antama suuntatieto röntgensironnasta määritettyyn konformaatiomuutoksen suuruuteen. Toisessa osajulkaisussa määritettiin proteiiniosasten paikka elektronimikroskopian avulla luodussa virusmallissa neutronisironnan ja kontrastivariaation avulla. Kolmessa viimeisessä osajulkaisussa esitetään uusi malli vihreiden bakteerien fotosynteettisen kompleksin antenniosan rakenteelle ja sen todetaan olevan sopusoinnussa useista eri bakteerilajeista saatujen röntgensironta- ja elektronimikroskopiatulosten kanssa. Karotenoidien vaikutusta rakenteeseen tutkittiin soveltamalla edellä mainittuja menetelmiä bakteereihin, joiden karotenoidisynteesiin vaikuttavat entsyymit oli poistettu geneettisin menetelmin

Three-dimensional reconstruction of Heterocapsa circularisquama RNA virus by cryo-electron microscopy

Heterocapsa circularisquama RNA virus is a non-enveloped icosahedral ssRNA virus infectious to the harmful bloom-forming dinoflagellate, H. circularisquama, and which is assumed to be the major natural agent controlling the host population. The viral capsid is constructed from a single gene product. Electron cryo-microscopy revealed that the virus has a diameter of 34 nm and T53 symmetry. The 180 quasi-equivalent monomers have an unusual arrangement in that each monomer contributes to a ‘bump’ on the surface of the protein. Though the capsid protein probably has the classic ‘jelly roll’ b-sandwich fold, this is a new packing arrangement and is distantly related to the other positive-sense ssRNA virus capsid proteins. The handedness of the structure has been determined by a novel method involving high resolution scanning electron microscopy of the negatively stained viruses and secondary electron detection

Image processing and computing in structural biology

With the help of modern techniques of imaging processing and computing, image data obtained by electron cryo-microscopy of biomolecules can be reconstructed to three-dimensional biological models at sub-nanometer resolution. These models allow answering urgent problems in life science, for instance, the pathways directing the self-recovery system of cell, which certainly has great significance for all our lives. To determine these models, there are two main electron microscopic methods available, corresponding to its two main modes of operation: 3DEM single particle reconstruction and electron diffraction. This thesis focuses on the research and methods of 3DEM and electron diffraction, and its practical application in solving the structure of a 50S ribosomal complex, which clarifies the mechanism of cell recovery in heat shock stress. Preliminary research on a novel structure determination method by using nano-crystals resulted in a novel software suite __ EDiff __ which is a program for unit cell parameter determination, indexing and so on.Cyttron ProjectUBL - phd migration 201

Three-Dimensional Aberration-Corrected Scanning Transmission Electron Microscopy for Biology

Recent instrumental developments have enabled greatly improved resolution of scanning transmission electron microscopes (STEM) through aberration correction. An additional and previously unanticipated advantage of aberration correction is the greatly improved depth sensitivity that has led to the reconstruction of a three-dimensional (3D) image from a focal series. In this chapter the potential of aberration-corrected 3D STEM to provide major improvements in the imaging capabilities for biological samples will be discussed. This chapter contains a brief overview ofthe various high-resolution 3D imaging techniques, a historical perspective of the development of STEM, first estimates of the dose-limited axial and lateral resolution on biological samples and initial experiments on stained thin sections

Solving Challenging Structures using Single-Particle Cryogenic Electron Microscopy

Single-particle cryogenic electron microscopy (cryo-EM) has become a powerful mainstay tool in high resolution structural biology thanks to advances in hardware, software and sample preparation technology. In my thesis, I utilized this technique to unravel the function of various challenging biological macromolecules. My first focus was bacterial ribosomal biogenesis: understanding how bacteria assemble their ribosomes. Ribosomes are the factories of the cell, responsible for manufacturing all proteins. Ribosomes themselves are huge, with the bacterial version made of 52 proteins and 4566 RNA nucleotides. How these components assemble has long been a mystery. Early groundbreaking work sketched out a biogenesis pathway using purified components in vitro – but under non-physiological conditions. We sought to understand how the bacterial ribosome – specifically the large subunit 50S – is built inside the cell. To achieve this, we engineered a conditional knock-out bacterial strain that lacked one specific ribosomal protein (L17). This caused the cells to accumulate incomplete intermediates along the 50S biogenesis pathway. These intermediates were purified and examined with mass spectrometry and single-particle cryo-EM. Two major hurdles arose in this project: firstly, the biogenesis intermediates exhibited a preferred orientation when vitrified for cryo-EM analysis. This means that instead of showing many different views required for reconstruction of the 3D structure, the intermediates only adopted one view on the cryo-EM grid. To overcome this problem, we engineered a method to induce additional views on the microscope by tilting the stage. Using another test protein that also exhibited preferred orientation (hemagglutinin), we optimized and characterized this new tilt methodology and showed it was generally applicable to overcoming preferred orientation, regardless of type of specimen. We also created a software tool, called 3DFSC (3dfsc.salk.edu), for other microscopists to calculate the degree of directional anisotropy in their structures due to preferred orientation. Using this tilt strategy finally enabled the structural elucidation of our 50S intermediates. The second challenge in the project was the large amount of heterogeneity present in the sample. Through hierarchical 3D classification schemes using the latest software tools, we obtained 14 different 50S intermediate structures, all from imaging a single cryo-EM grid. By analyzing the missing components of each intermediate, and corroborating these observations with mass spectrometry data, we outlined the first in vivo 50S assembly pathway, and showed that ribosome assembly occurs step-wise and in parallel pathways. My second focus was on pushing the resolution limits of single-particle cryo-EM using adeno-associated virus (AAV) serotype 2 homogeneous virus-like particles (VLPs) that lack DNA. Exploiting several technical advances to improve resolution, including use of gold grids, per-particle CTF refinement, and correction for Ewald sphere curvature, we managed to obtain a 1.86 Å resolution reconstruction of the AAV2L336C variant VLP, the highest resolution icosahedral virus reconstruction solved by single-particle cryo-EM to date. Using our structure, we were able to show improvements using Ewald sphere curvature correction and shed light on the mechanistic basis as to why the L336C mutation resulted in defects in genome packaging and infectivity compared to the WT viral particles. My third focus was the understanding of small membrane proteins involved in infectious diseases. Membrane proteins are a challenge to work with due to the need for them to be extracted from the lipid bilayer for studies as compared to soluble proteins. Infectious diseases have a huge burden on society, with the top three infectious agents accounting for 2.7 million deaths in 2016. The third most deadly infectious disease is malaria, a mosquito-borne parasite which kills 450,000 people annually. One drug used early on for treating malaria was chloroquine but its usefulness waned due to development of resistance. Chloroquine resistance is mediated by the chloroquine resistance transporter (PfCRT). Although small (49 kDa) for single-particle cryo-EM, we solved its structure by using fragment antibody technology to add mass and help with image alignment and 3D reconstruction. The 3.2 Å structure resembles other drug metabolite transporters, and the chloroquine resistance mutations map to a ring around the central cavity, suggesting this central pore as the drug binding site. Tuberculosis (TB) is the top killer, above malaria and HIV/AIDS, being responsible for 1.3 million deaths. In TB, a common antibiotic target is the bacterium’s cell wall synthesis machinery. One family of such enzymes is the arabinosyltransferases, which synthesize the critical arabinose sugars. Using single-particle cryo-EM, we solved two high resolution structures of one such essential enzyme, AftD. Due to the low yield of the protein, a picoliter automated sample dispensing robot was crucial to allow for initial cryo-EM analysis. We then performed mutagenesis studies in M. smegmatis, a TB model organism, which uncovered the critical amino acid residues in the active site and determined that a bound acyl-carrier-protein was likely involved in allosteric inhibition of AftD’s active site. Another member of the family, EmbB, is the target of a widely used frontline TB drug called ethambutol. We have solved the high resolution structures of the apo and putative drug-bound states of EmbB, allowing us to map out, for the first time, both the active site and drug-resistance mutations of this crucial enzyme. The atomic structures of the functional pockets of Mycobacterial AftD and malarial PfCRT will hopefully enable structure-based drug design to improve existing drugs or potentially even develop new treatments against these infectious maladies. In conclusion, the continual and breathtaking improvements in single-particle cryo-EM methodology has been instrumental in allowing the elucidation of the aforementioned biological macromolecules from ribosome biogenesis intermediates, to AAV2 vehicle, Plasmodium drug resistance transporter to mycobacterial glycosyltransferases – structures of which help explain biological function

The feasibility of high resolution, three-dimensional reconstruction of metal-coated surfaces in structural biology

>Magister Scientiae - MScLife is an emergent property of a complex network of interacting cellular-machines. Three-dimensional (3D), cellular structure captured at supra-atomic resolution has the potential to revolutionise our understanding of the interactions, dynamics and structure of these machines: proteins, organelles and other cellular constituents, in their normal functional states. Techniques, capable of acquiring 3D cellular structure at sufficient resolution to enable identification and interpretation of individual macromolecules in the cellular milieu, have the potential to provide this data. Advances in cryo-preservation, preparation and metal-coating techniques allow images of the surfaces of in situ macromolecules to be obtained in a life-like state by field emission scanning – and transmission electron microscopy (FE/SEM, FE/TEM) at a resolution of 2-4 nm. A large body of macromolecular structural information has been obtained using these techniques, but while the images produced provide a qualitative impression of three-dimensionality, computational methods are required to extract quantitative 3D structure. In order to test the feasibility of applying various photogrammetric and tomographic algorithms to micrographs of well-preserved metal-coated biological surfaces, several algorithms were attempted on a variety of FE/SEM and TEM micrographs. A stereoscopic algorithm was implemented and applied to FESEM stereo images of the nuclear pore basket, resulting in a high quality digital elevation map. A SEM rotation series of an object of complicated topology (ant) was reconstructed volumetrically by silhouette-intersection. Finally, the iterative helical real-space reconstruction technique as applied to cryo-TEM micrographs of unidirectionally heavy-metal shadowed. These preliminary results confirm that 3D information obtained from multiple TEM or SEM surface images could be applied to the problem of 3D macromolecular imaging in the cellular context. However, each of the various methods described here comes with peculiar topological, resolution and geometrical limitations, some of which are inherent shortcomings of the methodologies described; others might be overcome with improved algorithms. Combined with carefully designed surface experiments, some of the methods investigated here could provide novel insights and extend current surface-imaging studies. Docking of atomic resolution structures into low-resolution maps derived from surface imaging experiments is a particularly exciting prospect