Integrative structural modeling of macromolecular complexes using Assembline

2021 ◽  
Author(s):  
Vasileios Rantos ◽  
Kai Karius ◽  
Jan Kosinski
Author(s):  
D.W. Andrews ◽  
F.P. Ottensmeyer

Shadowing with heavy metals has been used for many years to enhance the topological features of biological macromolecular complexes. The three dimensional features present in directionaly shadowed specimens often simplifies interpretation of projection images provided by other techniques. One difficulty with the method is the relatively large amount of metal used to achieve sufficient contrast in bright field images. Thick shadow films are undesirable because they decrease resolution due to an increased tendency for microcrystalline aggregates to form, because decoration artefacts become more severe and increased cap thickness makes estimation of dimensions more uncertain.The large increase in contrast provided by the dark field mode of imaging allows the use of shadow replicas with a much lower average mass thickness. To form the images in Fig. 1, latex spheres of 0.087 μ average diameter were unidirectionally shadowed with platinum carbon (Pt-C) and a thin film of carbon was indirectly evaporated on the specimen as a support.


Author(s):  
B. Carragher ◽  
M. Whittaker

Techniques for three-dimensional reconstruction of macromolecular complexes from electron micrographs have been successfully used for many years. These include methods which take advantage of the natural symmetry properties of the structure (for example helical or icosahedral) as well as those that use single axis or other tilting geometries to reconstruct from a set of projection images. These techniques have traditionally relied on a very experienced operator to manually perform the often numerous and time consuming steps required to obtain the final reconstruction. While the guidance and oversight of an experienced and critical operator will always be an essential component of these techniques, recent advances in computer technology, microprocessor controlled microscopes and the availability of high quality CCD cameras have provided the means to automate many of the individual steps.During the acquisition of data automation provides benefits not only in terms of convenience and time saving but also in circumstances where manual procedures limit the quality of the final reconstruction.


2020 ◽  
Vol 477 (2) ◽  
pp. 459-459
Author(s):  
Lalith K. Chaganti ◽  
Shubhankar Dutta ◽  
Raja Reddy Kuppili ◽  
Mriganka Mandal ◽  
Kakoli Bose

Author(s):  
Svetlana L. Sazanova

Entrepreneurship plays an important role in the modern global economy; the share of products of small and medium enterprises in the gross product and exports not only of the developed but also of developing countries is growing. Innovation processes cover all sectors of the economy, and more and more people are involved in entrepreneurial activity, which contributes to the penetration of entrepreneurial thinking and business values in all areas of the socioeconomic life of society. The Institute of Entrepreneurship plays an increasingly prominent role in the institutional environment of socio-economic systems. This actualizes the problem of studying the relationship of the institution of entrepreneurship with the institutions of law, culture, management. This requires a methodology that allows you to explore the impact on the institute of entrepreneurship not only economic, but also non-economic factors. The methodology of the “old” institutionalism possesses such a tool, it is structural modeling (pattern modeling), which allows to explore the diversity of interrelationships of the institution of entrepreneurship with other components of the institutional and economic environment. The article explored the features of the development of the institution of entrepreneurship in Russia, established the relationship between the institution of entrepreneurship, values, motives and incentives for entrepreneurial activity, built a structural model of the institution of entrepreneurship based on the methodology of the old institutionalism (pattern modeling). The structural model of the institution of entrepreneurship reveals the relationship between the institution of entrepreneurship, the values of entrepreneurial activity, its motives and incentives; as well as the relationship between the institution of entrepreneurship with the institutions of governance, cultural and religious institutions, legal institutions and society.


2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>


2011 ◽  
Vol 38 (1) ◽  
pp. 28-35 ◽  
Author(s):  
Jin-Lan WANG ◽  
Lu-Shan WANG ◽  
Wei-Feng LIU ◽  
Guan-Jun CHEN ◽  
Pei-Ji GAO

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