Detection of Innersphere Interactions between Magnesium Hydrate and the Phosphate Backbone of the HDV Ribozyme Using Raman Crystallography

Gong, Bin; Chen, Yuanyuan; Christian, Eric L.; Chen, Jui Hui; Chase, Elaine; Chadalavada, Durga M.; Yajima, Rieko; Golden, Barbara L.; Bevilacqua, Philip C.; Carey, Paul R.

doi:10.1021/ja801861s

Cited by 41 publications

(91 citation statements)

References 20 publications

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“…In fact, among the available metallomacronutrients, Na(I), K(I), Mg(II) and Ca(II), in living systems, nature selected Mg(II) as the cofactor for the vast majority of enzymes that catalyze the breakage of (P)O-P(O) bonds. It appears important that experimental studies via XRD, MQMAS, ESIMS, Raman crystallography like those reported in Refs [10,[39][40][41][42], as well as theoretical studies like those reported in Refs 11,[43][44][45], are more and more performed on Mg(II)-NTPs and -NDPs species with the aim to shed light on the mobility of the metal on (di)triphosphate chain, on the role of free and metal bound water molecules, on the role of third molecules (mostly aminoacid residues) able to interact with the metal ions proximal to nucleotides and with nucleotides themselves. The structural role of the second divalent cation in biological systems that catalyze reactions on nucleotides (see for example Refs [46][47][48][49]), are worthy of more efforts too, on the basis of structure for 1 and 2 and of recent structures deposited in the PDB.…”

Section: Resultsmentioning

confidence: 97%

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

Tamasi¹,

Berrettini²,

Hursthouse³

et al. 2010

TOCRYJ

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Abstract:The X-ray diffraction (XRD) structures for new isoforms of [M(H 2 O) 6 ]·[M(HATP) 2 ]·2(HDPA)·xH 2 O, ATP = adenosine 5'-triphosphate, DPA = 2,2'-dipyridylamine, M = Mg(II), x = 6H 2 O, 1, M = Ca(II), x = 8H 2 O, 2 were determined by using rotating anode on molybdenum target X-ray source and Kappa CCD with confocal focusing mirror. The accuracy of the presently refined structure for 1 is the highest reported so far based on agreement factors (R1 = 0.0579) and estimated standard deviations (esds) on geometrical parameters. The comparative analysis was extended to the structures of other low molecular weight metal-triphosphate complexes, to the structures of metal-triphosphate-protein systems as well as to computed models of metal-triphosphate complexes. The structures of 1 and 2 reported in this work show that on changing the number of co-crystallized water molecules, the interaction of the metal to the phosphate chain (for 1) and the conformation of ribose (for 2) undergo subtle but significant changes. Interestingly, the vast majority of Mg-nucleoside triphosphate (NTP)-enzyme systems have similar pattern of coordination to the phosphate chain when compared to 1 and 2. The three phosphate groups have variable M-O bond distances, depending on the systems. The structures for 1 and 2 have a high significance as general model compounds for experimental solid state and computations for these types of biological systems.

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Section: Resultsmentioning

confidence: 97%

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

Tamasi¹,

Berrettini²,

Hursthouse³

et al. 2010

TOCRYJ

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“…Additionally, there is a negative feature that precedes the positive node for several crowders leading to a so-called differential feature ( Fig. 4B; Gong et al 2008). The negative feature arises because the melting of the tRNA in the presence of the crowder is over a narrower temperature range, reflective of the sharpening of a transition as associated with RNA folding cooperativity.…”

Section: Phementioning

confidence: 97%

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

Strulson

Boyer

Whitman

et al. 2014

RNA

Self Cite

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Folding mechanisms of functional RNAs under idealized in vitro conditions of dilute solution and high ionic strength have been well studied. Comparatively little is known, however, about mechanisms for folding of RNA in vivo where Mg 2+ ion concentrations are low, K + concentrations are modest, and concentrations of macromolecular crowders and low-molecular-weight cosolutes are high. Herein, we apply a combination of biophysical and structure mapping techniques to tRNA to elucidate thermodynamic and functional principles that govern RNA folding under in vivo-like conditions. We show by thermal denaturation and SHAPE studies that tRNA folding cooperativity increases in physiologically low concentrations of Mg 2+ (0.5-2 mM) and K + (140 mM) if the solution is supplemented with physiological amounts (∼20%) of a water-soluble neutral macromolecular crowding agent such as PEG or dextran. Low-molecular-weight cosolutes show varying effects on tRNA folding cooperativity, increasing or decreasing it based on the identity of the cosolute. For those additives that increase folding cooperativity, the gain is manifested in sharpened two-state-like folding transitions for full-length tRNA over its secondary structural elements. Temperaturedependent SHAPE experiments in the absence and presence of crowders and cosolutes reveal extent of cooperative folding of tRNA on a nucleotide basis and are consistent with the melting studies. Mechanistically, crowding agents appear to promote cooperativity by stabilizing tertiary structure, while those low molecular cosolutes that promote cooperativity stabilize tertiary structure and/or destabilize secondary structure. Cooperative folding of functional RNA under physiological-like conditions parallels the behavior of many proteins and has implications for cellular RNA folding kinetics and evolution.

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“…In addition to numerous studies of self-cleavage by the cisacting genomic and antigenomic HDV ribozymes (Been and Wickham 1997;Perrotta et al 1999aPerrotta et al ,b, 2006Wadkins et al 1999;Nakano et al 2000Nakano et al , 2003Shih and Been 2002;Harris et al 2004;Been 2006;Chadalavada et al 2007;Gong et al 2007Gong et al , 2009Sefcikova et al 2007a,b;Cerrone-Szakal et al 2008;Gong et al 2008;Chen et al 2009), significant work has also been performed to investigate trans-acting forms of this ribozyme for enzymology and therapeutic purposes (Been 1994;Luptak et al 2001;Harris et al 2002;Pereira et al 2002;Jeong et al 2003;Tinsley et al 2003Tinsley et al , 2004Das and Piccirilli 2005;Tinsley and Walter 2007;Walter and Perumal 2009). Generally, trans-acting HDV ribozymes exhibit a 1-2 order-of-magnitude slower catalytic rate constant compared to their cis-acting counterparts, likely due to a less tightly knit structure (Tinsley and Walter 2007).…”

Section: Introductionmentioning

confidence: 99%

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

Sripathi

Tay

Banáš

et al. 2014

RNA

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The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre-and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2 ′ -oxygens near the scissile phosphate compromise catalytic in-line fitness. A cisacting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape.

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Detection of Innersphere Interactions between Magnesium Hydrate and the Phosphate Backbone of the HDV Ribozyme Using Raman Crystallography

Cited by 41 publications

References 20 publications

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

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