The emerging role of MS in structure elucidation of protein–nucleic acid complexes

2008 ◽  
Vol 36 (4) ◽  
pp. 723-731 ◽  
Author(s):  
Yuliya Gordiyenko ◽  
Carol V. Robinson

Developments in MS enable us to apply this technique to non-covalent complexes, defining their stoichiometry, subunit interactions and architectural organization. We illustrate the application of this non-covalent MS approach to uncovering the overall topological arrangements of subunits and interactions within RNA–protein complexes studied in our laboratory over the last 5 years. These studies exemplify the emerging role and potential of MS as a complementary structural biology methodology and demonstrate its unique niche in investigations of dynamic or heterogeneous protein–nucleic acid complexes, which are not accessible to classical high-resolution structural biology techniques.

FEBS Journal ◽  
2006 ◽  
Vol 273 (7) ◽  
pp. 1463-1475 ◽  
Author(s):  
Sheila M. B. Lima ◽  
Ana Carolina Q Vaz ◽  
Theo L. F. Souza ◽  
David S. Peabody ◽  
Jerson L. Silva ◽  
...  

2020 ◽  
Vol 4 (3) ◽  
pp. 355-364
Author(s):  
M. Sankaranarayanan ◽  
Timothy T. Weil

Drosophila eggs are highly polarised cells that use RNA–protein complexes to regulate storage and translational control of maternal RNAs. Ribonucleoprotein granules are a class of biological condensates that form predominantly by intracellular phase separation. Despite extensive in vitro studies testing the physical principles regulating condensates, how phase separation translates to biological function remains largely unanswered. In this perspective, we discuss granules in Drosophila oogenesis as a model system for investigating the physiological role of phase separation. We review key maternal granules and their properties while highlighting ribonucleoprotein phase separation behaviours observed during development. Finally, we discuss how concepts and models from liquid–liquid phase separation could be used to test mechanisms underlying granule assembly, regulation and function in Drosophila oogenesis.


2019 ◽  
Vol 47 (W1) ◽  
pp. W462-W470 ◽  
Author(s):  
Broto Chakrabarty ◽  
Varun Naganathan ◽  
Kanak Garg ◽  
Yash Agarwal ◽  
Nita Parekh

Abstract Network theory is now a method of choice to gain insights in understanding protein structure, folding and function. In combination with molecular dynamics (MD) simulations, it is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc. Updated version of NAPS now facilitates network analysis of the complete repertoire of these biomolecules, i.e., proteins, protein–protein/nucleic acid complexes, MD trajectories, and RNA. Various options provided for analysis of MD trajectories include individual network construction and analysis of intermediate time-steps, comparative analysis of these networks, construction and analysis of average network of the ensemble of trajectories and dynamic cross-correlations. For protein–nucleic acid complexes, networks of the whole complex as well as that of the interface can be constructed and analyzed. For analysis of proteins, protein–protein complexes and MD trajectories, network construction based on inter-residue interaction energies with realistic edge-weights obtained from standard force fields is provided to capture the atomistic details. Updated version of NAPS also provides improved visualization features, interactive plots and bulk execution. URL: http://bioinf.iiit.ac.in/NAPS/


Author(s):  
David J. Aceti ◽  
Paul G. Blommel ◽  
Yaeta Endo ◽  
Brian G. Fox ◽  
Ronnie O. Frederick ◽  
...  

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