scholarly journals Structural modeling of protein–RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS

2017 ◽  
Vol 14 (5) ◽  
pp. 487-490 ◽  
Author(s):  
Georg Dorn ◽  
Alexander Leitner ◽  
Julien Boudet ◽  
Sébastien Campagne ◽  
Christine von Schroetter ◽  
...  
Keyword(s):  
Structural Modeling ◽  
Isotope Labeled Rna ◽  
Labeled Rna ◽  
Rna Complexes

Stable Isotope-Labeled RNA Phosphoramidites to Facilitate Dynamics by NMR

2015 ◽  
pp. 461-494 ◽  
Author(s):  
Christoph H. Wunderlich ◽  
Michael A. Juen ◽  
Regan M. LeBlanc ◽  
Andrew P. Longhini ◽  
T. Kwaku Dayie ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Isotope Labeled Rna ◽  
Labeled Rna

scholarly journals Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5581
Author(s):  
Lukasz T. Olenginski ◽  
Kehinde M. Taiwo ◽  
Regan M. LeBlanc ◽  
Theodore K. Dayie
Keyword(s):  
Building Blocks ◽  
Nmr Structure ◽  
Atomic Resolution ◽  
Line Broadening ◽  
Rna Molecules ◽  
Structure And Dynamics ◽  
Rna Analysis ◽  
Isotope Labeled Rna ◽  
Labeled Rna ◽  
Structural Research

RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.

Correction: Structural modeling and role of HAX-1 as a positive allosteric modulator of human serine protease HtrA2

2020 ◽  
Vol 477 (2) ◽  
pp. 459-459
Author(s):  
Lalith K. Chaganti ◽  
Shubhankar Dutta ◽  
Raja Reddy Kuppili ◽  
Mriganka Mandal ◽  
Kakoli Bose
Keyword(s):  
Serine Protease ◽  
Structural Modeling ◽  
Allosteric Modulator ◽  
Positive Allosteric Modulator

Structural Modeling of Institute of Entrepreneurship in Russia

2019 ◽  
pp. 34-48
Author(s):  
Svetlana L. Sazanova
Keyword(s):  
Global Economy ◽  
Structural Model ◽  
Institutional Environment ◽  
Small And Medium Enterprises ◽  
Structural Modeling ◽  
Entrepreneurial Activity ◽  
Pattern Modeling ◽  
Medium Enterprises ◽  
The Impact ◽  
The Relationship

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.

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<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>

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