Cryoelectron Microscopy As a Functional Instru- Ment for Systems
Total Page：16
File Type：pdf, Size：1020Kb
UDC 57.086.3:537.533.33 Cryoelectron Microscopy as a Functional Instru- ment for Systems Biology, Structural Analysis & Experimental Manipulations with Living Cells (A comprehensive review of the current works). Oleg V. Gradov INEPCP RAS, Moscow, Russia Email: [email protected] Margaret A. Gradova ICP RAS, Moscow, Russia Email: [email protected] Abstract — The aim of this paper is to give an introductory review of the cryoelectron microscopy as a complex data source for the most of the system biology branches, including the most I. TECHNICAL APPLICATIONS OF perspective non-local approaches known as "localomics" and "dynamomics". A brief summary of various cryoelectron mi- CRYOELECTRON MICROSCOPY croscopy methods and corresponding system biological ap- Since its development in early 1980s [31] proaches is given in the text. The above classification can be considered as a useful framework for the primary comprehen- cryo-electron microscopy has become one of sions about cryoelectron microscopy aims and instrumental the most functional research methods providing tools. We do not discuss any of these concepts in details, but the study of physiological and biochemical merely point out that their methodological complexity follows changes in living matter at various hierarchical only from the structure-functional complexity of biological levels from single mammalian cell morphology systems which are investigated in this manner. We also postu- late that one can employ some of the cryoelectron microscopic [108] to nanostructures [69] and even the struc- techniques not only for observation, but also for modification ture of biomacromolecules with a near-atomic and structural refunctionalization of some biological and similar resolution [19], i.e. at an all-atom configuration soft matter objects and microscopic samples. In other worlds, reconstruction [72]. In recent papers the cryo- we start with the cryoelectron microscopy as a tool for the sys- electron microscopic techniques were reported tem biology and progress to its applying as an instrument for system biology and functional biomimetics; i.e. "system cryobi- to achieve the effective resolution up to several ology" goes over into "synthetic cryobiology" or "cryogenic angstroms [12,71,130] and about 2-5 nm in a biomimetics". All these conclusions can be deduced from the 3D representation [29]. To date the structural most recent works of the latest years, including just submitted methods of cryo-electron microscopy have been foreign papers. This article provides an up-to-date description of involved in characterization of a number of the conceptual basis for the novel view on the computational cryoelectron microscopy (in silico) approaches and the data supramolecular structures and complexes: from mining principles which lie at the very foundation of modern the well-studied fibrillar collagen structures structural analysis and reconstruction. [92], intraflagillar transport complexes of pro- tozoa [91], tubulin in microtubules [125] and Index Terms — cryo-electron microscopy, cryo-electron to- some other fibrillar and filamentous structures mography, system biology, localomics, dynamomics, microm- achining, structural analysis, in silico, molecular machines with the relative molecular weight of about gigadalton [101] up to such subtle elements of biological machinery as ribosomal complexes Manuscript for the journal "Problems of Cryobiology and Cryomedicine”. (e.g. those involved in cotranslational folding and translocation [62]), elements of secondary 3. algorithms of subtomogram analysis [95] and supersecondary protein structure [7], and in cryo-electron tomography [15,54], as well as the conformational effects in molecu- 4. eigen analysis with the search for ei- lar mechanisms of their folding [25] and the genvectors in order to enable classification of mechanisms of expression in the complexes of the cryoelectron images upon their angular encoding semantides [109] (in terms of characteristics [106], Zuckerkandl and Pauling [133]). In addition to 5. wavelet methods using multivariate the conventional cryo-electron microscopy, functions and the Toeplitz structures [115], etc. modern structural analysis, particularly the de- Except the above mentioned methods termination of the protein secondary structure, there are also a number of widely used conven- requires the use of its precision 3D analog – tional methods of structural and chemical pro- cryo-electron tomography [9], which enables filing (e.g. "cryo-ultra-low-angle microtomy") structure visualization at a wide scale / range of [45] and other similar methods, underlying the sizes, including the all-atom mapping [88] and a CEDX (quantitative cryo-analytical scan- nanoscale cytophysiological ultrastructure anal- ning electron microscopy) approaches [78]. In ysis (so-called nanoimaging [63]. There is also other words, modern cryo-electron microscopic an inherently close method of cryo-tomography techniques are mostly automated data pro- – X-ray tomography with cooling under high cessing and interpretation methods, rather than pressure [123], which demonstrates approxi- data acquisition. mately the same metrological characteristics. The above statement can be illustrated us- ing the data provided by M. Stowell from the II. ALGORITHMIC TOOLS FOR University of Cоlоrаdо. It is seen from the Fig. CRYO-ELECTRON MICROSCOPY 1 that even the similar structures with the equivalent morphometric parameters can It is noteworthy that the ultra-high meas- demonstrate a high dispersion of geometrical urement accuracy requires the use of advanced characteristics, and in the case of different itera- mathematical apparatus and algorithmic pro- tions of the mathematical and statistical data cessing: even the so-called direct methods of processing one can expect to obtain different improving the image quality in cryo-electron morphologies and even different topologies (ac- microscopy are implemented only through the cording to the number of connections) of the optimization of the number of summed and cor- object under 3D reconstruction. The dynamics responding files with the unary cryo-electron of the increase in accuracy of the measurements micrographs [65,46]. This procedure requires a and morphological reconstructions from 1990 to significant amount of computer time and robust 2000 was demonstrated by J. Frank in 2006 (see high-performance mathematical processing sys- Fig. 2), which may be attributed to the im- tems. The modern trend in the hardware for provement of the mathematical data processing such processing places a special emphasis on methods. Thus, it is clear that the ambiguity of the CUDA technologies using video cards / the structures' morphology after reconstruction graphics processing units (GPUs) providing the in cryo-electron microscopy and tomography is improvement of calculations [52], while for the characterized not only by quantitative (mor- purposes of data processing in cryo-electron phometric), but also by qualitative (geometric microscopy in addition to the standard princi- and topological) transformations. ples of machine learning in the pattern recogni- Moreover, an ambiguous data interpreta- tion [105,85] it is also useful to apply the fol- tion in cryo-electron microscopic structure lowing approaches: analysis necessitates the use of various mathe- 1. flexible variants of the parameter fitting matical models which determine the achieved by retraining during the search for ex- morphostructural representation of the result tremes [3], obtained, i.e. the above models may be one-to- 2. Bayesian probabilistic approaches in one corresponded to the methods of data pro- cryo-electron structural analysis [97], cessing. Thus, there are several reports on cryo- electron microscopy using molecular dynamics cellular dynamic interactions using cryo- simulations corresponding to flexible fitting electron tomography [59] and a so-called "4D methods [23]; pseudoatomic models corre- cryo-electron microscopy of proteins" [37]. Fur- sponding to various approaches to the interpre- thermore, in immunomics [16,112], considering tation of full-atom structural analysis data on the traditional use of a synchronous time-lapse the angstrom resolution [84]; probabilistic 3D cinematographic equipment in immuno-electron models of single particles, corresponding to the microscopy [8], it is reasonable to introduce probabilistic (partly Bayesian) methods of data dynamic cryo-electron measurements into cryo- processing [35], etc. The simulation process immuno-electron microscopy [89], which at the should consider or derive ab initio the sample same time will allow to avoid the image "blur- characteristics (namely, its solvation shell or a ring" artifacts by using the previous frames as hydration layer [100]), as well as the noise sim- the references for the reconstruction of the ob- ulation and the correction of the metrological ject shape and structure [18]. readings drift [102] considering the process of It would be also useful to consider some image capturing [116]. With the increasing role more examples illustrating the applicability of of the model interpretation in cryo-EM data cryo-electron microscopy as a multivariate in- processing [76] there is a significant increase in strument in systems biology. First of all it con- the level of conjugation between modeling, cerns the investigations in membranomics and docking (selection of the most favorable molec- viromics. Ultrastructural studies of ular orientation for the stable complex