Using Analytical Ultracentrifugation (AUC) to Measure Global Conformational Changes Accompanying Equilibrium Tertiary Folding of RNA Molecules

Author(s):  
Somdeb Mitra
Author(s):  
Lev Levintov ◽  
Harish Vashisth

Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response to various environmental stimuli including temperature, pH, and ligands. In particular, viral RNA molecules are a key example...


1999 ◽  
Vol 96 (16) ◽  
pp. 9077-9082 ◽  
Author(s):  
T. Ha ◽  
X. Zhuang ◽  
H. D. Kim ◽  
J. W. Orr ◽  
J. R. Williamson ◽  
...  

2020 ◽  
Author(s):  
Martín González Buitrón ◽  
Ronaldo Romario Tunque Cahui ◽  
Emilio García Ríos ◽  
Layla Hirsh ◽  
María Silvina Fornasari ◽  
...  

AbstractConformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function.We have developed CoDNaS-RNA as the first database of conformational diversity in RNA molecules. Known RNA structures are retrieved and clustered to identify alternative conformers of each molecule. Pairwise structural comparisons within each cluster allows to measure the variability of the molecule. Additional data on structural features, molecular interactions and functional annotations are provided. CoDNaS-RNA is implemented as a public resource that can be of much interest for computational and bench scientists alike.AvailabilityCoDNaS-RNA is freely accessible at http://ufq.unq.edu.ar/[email protected]


2005 ◽  
Vol 52 (2) ◽  
pp. 469-476 ◽  
Author(s):  
Adam Sobczak ◽  
Magdalena Blazejczyk ◽  
Grzegorz Piszczek ◽  
Gang Zhao ◽  
Jacek Kuznicki ◽  
...  

The EF-hand Ca(2+)-binding protein calmyrin is expressed in many tissues and can interact with multiple effector proteins, probably as a sensor transferring Ca(2+) signals. As oligomerization may represent one of Ca(2+)-signal transduction mechanisms, we characterised recombinant calmyrin forms using non-reducing SDS/PAGE, analytical ultracentrifugation and gel filtration. We also aimed at identification of biologically active calmyrin forms. Non-reducing SDS/PAGE showed that in vitro apo- and Ca(2+)-bound calmyrin oligomerizes forming stable intermolecular disulfide bridges. Ultracentrifugation indicated that at a 220 microM initial protein concentration apo-calmyrin existed in an equilibrium of a 21.9 kDa monomer and a 43.8 kDa dimer (trimeric or tetrameric species were not detected). The dimerization constant was calculated as Ka = 1.78 x 103 M(-1) at 6 degrees C. Gel filtration of apo- and Ca(2+)-bound calmyrin at a 100 microM protein concentration confirmed an equilibrium of a monomer and a covalent dimer state. Importantly, both monomer and dimer underwent significant conformational changes in response to binding of Ca(2+). However, when calmyrin forms were analyzed under non-reducing conditions in cell extracts by Western blotting, only monomeric calmyrin was detected in human platelets and lymphocytes, and in rat brain. Moreover, in contrast to recombinant calmyrin, crosslinking did not preserve any dimeric species of calmyrin regardless of Ca(2+) concentrations. In summary, our data indicate that although calmyrin forms stable covalent dimers in vitro, it most probably functions as a monomer in vivo.


2016 ◽  
Vol 473 (23) ◽  
pp. 4473-4491 ◽  
Author(s):  
Ka Wai Fung ◽  
David W. Wright ◽  
Jayesh Gor ◽  
Marcus J. Swann ◽  
Stephen J. Perkins

During the activation of complement C4 to C4b, the exposure of its thioester domain (TED) is crucial for the attachment of C4b to activator surfaces. In the C4b crystal structure, TED forms an Arg104–Glu1032 salt bridge to tether its neighbouring macroglobulin (MG1) domain. Here, we examined the C4b domain structure to test whether this salt bridge affects its conformation. Dual polarisation interferometry of C4b immobilised at a sensor surface showed that the maximum thickness of C4b increased by 0.46 nm with an increase in NaCl concentration from 50 to 175 mM NaCl. Analytical ultracentrifugation showed that the sedimentation coefficient s20,w of monomeric C4b of 8.41 S in 50 mM NaCl buffer decreased to 7.98 S in 137 mM NaCl buffer, indicating that C4b became more extended. Small angle X-ray scattering reported similar RG values of 4.89–4.90 nm for C4b in 137–250 mM NaCl. Atomistic scattering modelling of the C4b conformation showed that TED and the MG1 domain were separated by 4.7 nm in 137–250 mM NaCl and this is greater than that of 4.0 nm in the C4b crystal structure. Our data reveal that in low NaCl concentrations, both at surfaces and in solution, C4b forms compact TED–MG1 structures. In solution, physiologically relevant NaCl concentrations lead to the separation of the TED and MG1 domain, making C4b less capable of binding to its complement regulators. These conformational changes are similar to those seen previously for complement C3b, confirming the importance of this salt bridge for regulating both C4b and C3b.


1975 ◽  
Author(s):  
A. Molla ◽  
H. Claeys ◽  
D. Collen

Bovine Hageman factor (factor XII) was obtained in inactive form from fresh plasma with a recovery of 54.7±9.0 per cent and a yield of 16.3±2.9 mg per liter. The specific activity after activation with kaolin, determined with Hageman factor deficient human plasma, was 35.6±2.6 units (the activity of 1 ml fresh BaSO4-adsorbed bovine plasma) per mg protein.Analytical ultracentrifugation revealed a homogeneous protein with a sedimentation coefficient of 4.36. The extinction coefficient (A280 nm %) was 14.4, and the NH2-terminal residue Ala (0.6 mole/mole determined as Dns-Ala). SDS-polyacrylamide gel electrophoresis (PAGE) in the presence of dithiothreitol revealed a doublet with an average estimated mol wt of 76,000 and a difference of less than 5,000 between the two forms. Chemical analysis revealed (in moles per mole) Met: 2; His: 59; Lys: 28; Arg: 32 and sialic acid: 13 (thio-barbituric acid assay), hexose: 26 (orcinol method). PAGE at pH 2.5 revealed two and PAGE at pH 8.3 six main bands.Over 90 per cent of the purified iodine-labeled protein was adsorbed on celite. About 95 per cent of the enzyme activity was destroyed by incubation with 10−2 M di-iso-propylfluorophosphate (DFP) for 24 hr at room temperature. Between 65 and 85 per cent of the protein was eluted from the celite with 5% SDS. Both the NH2-terminal residue and the mol wt of the eluted protein were unchanged suggesting that activation of the proenzyme is the result of conformational changes with exposure of an active center serine residue. Measurements of radioactive DFP incorporation and COOH-terminal analysis, to prove this hypothesis are in progress.


2005 ◽  
Vol 6 (2) ◽  
pp. 127-134 ◽  
Author(s):  
Jonathan P. A. Wood ◽  
Stephanie A. Capaldi ◽  
Mark A. Robinson ◽  
Andrew J. Baron ◽  
Nicola J. Stonehouse

The use of bacteriophages as experimental tools allows the investigation of interactions between components at the molecular level that are often not possible in more complex virus systems. The bacteriophage φ29 acts as a molecular machine to package its own genomic DNA during viral assembly. Self-associating RNA molecules, called pRNA, have an essential role in the function of this machine. This paper reports the characterization of this self-association (which leads to multimerisation of wild-type and truncated variant pRNAs) by analytical ultracentrifugation (including determination of the partial specific volume of the pRNA), together with an investigation into the domains of the molecule important for multimerisation by the use of complementary DNA probes.


2013 ◽  
Vol 104 (2) ◽  
pp. 263a
Author(s):  
Bashkim Kokona ◽  
Ashton Shaffer ◽  
Mithila Rajagopal ◽  
Susan White

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Saminathan Ramakrishnan ◽  
Jason R. Stagno ◽  
Chelsie E. Conrad ◽  
Jienyu Ding ◽  
Ping Yu ◽  
...  

AbstractTime-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.


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