AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

Aduri, Raviprasad; Psciuk, Brian T.; Saro, Pirro; Taniga, Hariprakash; Schlegel, H. Bernhard; SantaLucia, John

doi:10.1021/ct600329w

Cited by 178 publications

(302 citation statements)

References 48 publications

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“…27 Aduri et al constructed a model of the E. coli 30S ribosome with all of the modifications present. 46 The results show that the methyl groups in m 2 G966 and m 5 C967 extend their stacking surface areas. The extended surface contact stabilizes the rather unusual 970 loop structure, which has few intra-loop H-bond interactions.…”

Section: Importance Of the 966 967 And 968 Stackmentioning

confidence: 91%

“…In addition, the methyl group of m 2 G966 is within van der Waals contact of Arg128 of protein S9 in the T. thermophilus 30S structure with m 2 G966 modeled in, suggesting that m 2 G966 stabilizes S9 binding through hydrophobic interactions. 19,24,46 The base of 966 interacts with the backbone of the P-site tRNA at position 34 20 and in the saturation mutagenesis showed a preference for purines. We found that among the functional mutants, adenosine was present more often than m 2 G at position 966.…”

Section: Importance Of the 966 967 And 968 Stackmentioning

confidence: 99%

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Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA

Saraiya¹,

Lamichhane

Chow

et al. 2008

Journal of Molecular Biology

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SummaryThe 970 loop (helix 31) of Escherichia coli 16S rRNA contains two modified nucleotides, m 2 G966 and m 5 C967. Positions A964, A969 and C970 are conserved among the Bacteria, Archaea and Eukarya. The nucleotides present at positions 965, 966, 967, 968 and 971, however, are only conserved and unique within each domain. All organisms contain a modified nucleoside at position 966, but the type of the modification is domain specific. Biochemical and structure studies have placed this loop near the P site and have shown it to be involved in the decoding process and in binding the antibiotic tetracycline. To identify the functional components of this rRNA hairpin, the eight nucleotides of the 970 loop of helix 31 were subjected to saturation mutagenesis and 107 unique functional mutants were isolated and analyzed. Non-random nucleotide distributions were observed at each mutated position among the functional isolates. Nucleotide identity at positions 966 and 969 significantly affects ribosome function. Ribosomes with single mutations of m 2 G966 or m 5 C967 produce more protein in vivo than wild-type ribosomes. Over-expression of initiation factor 3 (IF3) specifically restored wild-type levels of protein synthesis to the 966 and 967 mutants, suggesting that modification of these residues is important for IF3 binding and for the proper initiation of protein synthesis.

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Section: Importance Of the 966 967 And 968 Stackmentioning

confidence: 91%

Section: Importance Of the 966 967 And 968 Stackmentioning

confidence: 99%

Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA

Saraiya¹,

Lamichhane

Chow

et al. 2008

Journal of Molecular Biology

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“…Molecular Dynamics Simulations-Atomistic explicit solvent simulations of minimally structured U 5 (GC)U 5 , U 4 ⌿(GC)U 5 , U 5 (GC)⌿U 4 , and U 4 ⌿(GC)⌿U 4 RNA constructs were performed using the GROMACS (Groningen Machine for Chemical Simulations (29 -32) molecular dynamics package on the local ACISS (Applied Computational Instrument for Scientific Synthesis) cluster at the University of Oregon, using an AMBER (Assisted Model Building with Energy Refinement) (33) force field optimized for stem-loop RNA structures with modified force-field parameters for the ⌿ base (34). All simulations were performed in explicit solvent utilizing the spc/e water model and 150 mM NaCl with excess sodium ions to neutralize the system, Ewald summation for the electrostatics, and standard force-field cutoffs and parameters.…”

Section: Methodsmentioning

confidence: 99%

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

deLorimier

Hinman

Copperman

et al. 2017

Journal of Biological Chemistry

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Edited by Ronald C. WekMyotonic dystrophy type 2 is a genetic neuromuscular disease caused by the expression of expanded CCUG repeat RNAs from the non-coding region of the CCHC-type zinc finger nucleic acid-binding protein (CNBP) gene. These CCUG repeats bind and sequester a family of RNA-binding proteins known as Muscleblind-like 1, 2, and 3 (MBNL1, MBNL2, and MBNL3), and sequestration plays a significant role in pathogenicity. MBNL proteins are alternative splicing regulators that bind to the consensus RNA sequence YGCY (Y ‫؍‬ pyrimidine). This consensus sequence is found in the toxic RNAs (CCUG repeats) and in cellular RNA substrates that MBNL proteins have been shown to bind. Replacing the uridine in CCUG repeats with pseudouridine (⌿) resulted in a modest reduction of MBNL1 binding. Interestingly, ⌿ modification of a minimally structured RNA containing YGCY motifs resulted in more robust inhibition of MBNL1 binding. The different levels of inhibition between CCUG repeat and minimally structured RNA binding appear to be due to the ability to modify both pyrimidines in the YGCY motif, which is not possible in the CCUG repeats. Molecular dynamic studies of unmodified and pseudouridylated minimally structured RNAs suggest that reducing the flexibility of the minimally structured RNA leads to reduced binding by MBNL1. Myotonic dystrophy type 1 (DM1)3 is a genetic neuromuscular disease caused by expression of expanded CUG repeats in the 3Ј UTR of the dystrophia myotonica protein kinase (DMPK) gene. Similar to DM1, myotonic dystrophy type 2 (DM2) is caused by expression of expanded CCUG repeats in an intron of the CCHC-type zinc finger nucleic acid-binding protein (CNBP) gene. DM1 and DM2 occur when the CUG/CCUG repeats are expanded beyond 100 repeats, and patients can have up to thousands of CUG/CCUG repeats (1, 2). A primary component of the currently accepted DM1 and DM2 disease mechanism is that expanded CUG/CCUG repeats sequester RNAbinding proteins (primarily the Muscleblind-like family), which prevents these proteins from performing their functions in cells (3, 4).The members of the Muscleblind-like family of proteins (MBNL1, MBNL2, and MBNL3) bind RNA and regulate several RNA processing pathways, including alternative splicing, premiRNA biogenesis, mRNA localization, alternative polyadenylation, and circular RNA generation (5-9). MBNL proteins bind to the consensus YGCY RNA sequence (6, 10). CUG and CCUG repeats are composed of YGCY motifs creating hundreds or thousands of perfect MBNL-binding sites resulting in large numbers of MBNL proteins binding to the repeats and forming nuclear foci (11). When MBNL proteins are sequestered, they are unable to regulate RNA processing events, and consequently, many DM1 and DM2 symptoms are caused by misregulated alternative splicing and potentially the loss of other MBNL activities (12). It is therefore important to understand how MBNL proteins bind to their toxic and cellular RNA substrates to develop mechanisms to alleviate MBNL sequestration in DM1 and DM2.MBNL pro...

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“…All pairs were solvated and neutralized using the AMBER 9 xleap module to render the pairs. Modifications were added by replacing individual molecule designations in unmodified base Protein Data Bank (PDB) files with those from the RNA modified parameters database (Aduri et al 2007) and were matched by comparison using Chimera (Pettersen et al 2004) to produce new functional PDB files. Bases were initially minimized in vacuum to reach optimum geometries from which periodic restraint angles were determined.…”

Section: Methodsmentioning

confidence: 99%

Free energy calculation of modified base-pair formation in explicit solvent: A predictive model

Vendeix

Munoz²,

Agris³

2009

RNA

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The maturation of RNAs includes site-specific post-transcriptional modifications that contribute significantly to hydrogen bond formation within RNA and between different RNAs, especially in formation of mismatch base pairs. Thus, an understanding of the geometry and strength of the base-pairing of modified ribonucleoside 59-monophosphates, previously not defined, is applicable to investigations of RNA structure and function and of the design of novel RNAs. The geometry and free energies of base-pairings were calculated in aqueous solution under neutral conditions with AMBER force fields and molecular dynamics simulations (MDSs). For example, unmodified uridines were observed to bind to uridine and cytidine with significant stability, but the ribose C19-C19 distances were far short (;8.9 Å ) of distances observed for canonical A-form RNA helices. In contrast, 5-oxyacetic acid uridine, known to bind adenosine, wobble to guanosine, and form mismatch base pairs with uridine and cytidine, bound adenosine and guanosine with geometries and energies comparable to an unmodified uridine. However, the 5-oxyacetic acid uridine base paired to uridine and cytidine with a C19-C19 distance comparable to that of an A-form helix, ;11 Å , when a H 2 O molecule migrated between and stably hydrogen bonded to both bases. Even in formation of canonical base pairs, intermediate structures with a second energy minimum consisted of transient H 2 O molecules forming hydrogen bonded bridges between the two bases. Thus, MDS is predictive of the effects of modifications, H 2 O molecule intervention in the formation of base-pair geometry, and energies that are important for native RNA structure and function.

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AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

Cited by 178 publications

References 48 publications

Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA

Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

Free energy calculation of modified base-pair formation in explicit solvent: A predictive model

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