Predicting helical coaxial stacking in RNA multibranch loops

被引:51
作者
Tyagi, Rahul
Mathews, David H.
机构
[1] Univ Rochester, Med Ctr, Dept Biostat & Computat Biol, Rochester, NY 14642 USA
[2] Univ Rochester, Med Ctr, Dept Biochem & Biophys, Rochester, NY 14642 USA
关键词
coaxial stacking; RNA structure; multibranch loop; helical junction; dynamic programming; partition function; nearest-neighbor model;
D O I
10.1261/rna.305307
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The hypothesis that RNA coaxial stacking can be predicted by free energy minimization using nearest- neighbor parameters is tested. The results show 58.2% positive predictive value ( PPV) and 65.7% sensitivity for accuracy of the lowest free energy configuration compared with crystal structures. The probability of each stacking configuration can be predicted using a partition function calculation. Based on the dependence of accuracy on the calculated probability of the stacks, a probability threshold of 0.7 was chosen for predicting coaxial stacks. When scoring these likely stacks, the PPV was 66.7% at a sensitivity of 51.9%. It is observed that the coaxial stacks of helices that are not separated by unpaired nucleotides can be predicted with a significantly higher accuracy ( 74.0% PPV, 66.1% sensitivity) than the coaxial stacks mediated by noncanonical base pairs ( 55.9% PPV, 36.5% sensitivity). It is also shown that the prediction accuracy does not show any obvious trend with multibranch loop complexity as measured by three different parameters.
引用
收藏
页码:939 / 951
页数:13
相关论文
共 82 条
[51]   THE COMBINATION OF SYMBOLIC AND NUMERICAL COMPUTATION FOR 3-DIMENSIONAL MODELING OF RNA [J].
MAJOR, F ;
TURCOTTE, M ;
GAUTHERET, D ;
LAPALME, G ;
FILLION, E ;
CEDERGREN, R .
SCIENCE, 1991, 253 (5025) :1255-1260
[52]   Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure [J].
Mathews, DH ;
Disney, MD ;
Childs, JL ;
Schroeder, SJ ;
Zuker, M ;
Turner, DH .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (19) :7287-7292
[53]   Dynalign: An algorithm for finding the secondary structure common to two RNA sequences [J].
Mathews, DH ;
Turner, DH .
JOURNAL OF MOLECULAR BIOLOGY, 2002, 317 (02) :191-203
[54]   Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure [J].
Mathews, DH ;
Sabina, J ;
Zuker, M ;
Turner, DH .
JOURNAL OF MOLECULAR BIOLOGY, 1999, 288 (05) :911-940
[55]   A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria [J].
Miranda-Ríos, J ;
Navarro, M ;
Soberón, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) :9736-9741
[56]   AROMATIC STACKING INTERACTIONS IN AQUEOUS-SOLUTION - EVIDENCE THAT NEITHER CLASSICAL HYDROPHOBIC EFFECTS NOR DISPERSION FORCES ARE IMPORTANT [J].
NEWCOMB, LF ;
GELLMAN, SH .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994, 116 (11) :4993-4994
[57]  
NISSEN F, 1999, STRUCTURE, V7, P143
[58]   The structural basis of ribosome activity in peptide bond synthesis [J].
Nissen, P ;
Hansen, J ;
Ban, N ;
Moore, PB ;
Steitz, TA .
SCIENCE, 2000, 289 (5481) :920-930
[59]  
Norberg J, 1996, BIOPOLYMERS, V39, P765, DOI 10.1002/(SICI)1097-0282(199612)39:6<765::AID-BIP3>3.3.CO
[60]  
2-G