RNA Structure Prediction and Comparison. RNA Biology Background

Transcription

1 RN Structure Prediction and omparison Session 1 RN Biology Background édric Saule Faculty of Technology cedric.saule@ni-bielefeld.de pril 13, 2015 édric Saule

2 Overview of lecture topics The lecture plan has 5 parts... 1 RN biology (short) 2 RN structure prediction based on thermodynamics 3 omparative (multiple) structure prediction 4 Stochastic models 5 RN structure comparison 6 Selected special topics édric Saule

3 Literature There is no textbook on this topic yet. urrently, many authors are cooperting to write one. (Pr. R. iegerich wrote chapters on bstract Shape nalysis and Stochastic Models.) The slides of this lecture and related research articles will be made available via the lecture home page at StrukturSS15 édric Saule

4 Functional roles of RN The three classical roles of RN: mrna - the messenger RN: spelling the genetic code rrn - the ribosomal RN: performing protein synthesis trn - the transfer RN: linking codons to amino acids édric Saule

5 The (ancient) RN world hypothesis The only plausible theory about the origin of life sees RN as the early carrier of evolution This is solves the chicken-and-egg problem that proteins need DN to be encoded, and DN needs proteins to be processed. RN has both of these functions - it can store information (though less reliably than DN) it has catalytic activity (though less efficient than proteins) cording to the entral Dogma of molecular biology, all important functions in today s organism are carried out by proteins édric Saule

6 dversary observations Over the decades, a number of observations had been made which were inconsistent with the entral Dogma... a handful of RNs with enzymatic activity (hammerhead ribozyme) H/ and D-box sno-rns self-splicing introns the catalytic core of the ribosome is purely RN no protein nearby. many more see work by John Mattick... there were thought of as the exception to the rule. édric Saule

7 The fall of the entral Dogma and the advent of the New RN World The entral Dogma broke down around the year 2001/2002: The human genome project yielded an unxepected small number of protein-coding genes around , maybe less This small number of protein genes cannot explain organismic complexity of higher eucaryotes lternative splicing was perceived to be the rule rather than an exception, but it cannot create enough variety ttention was redirected to long-known facts about regulatory roles of RN The most prominent of those were mirns and RN interference édric Saule

8 The variety of RN functions The universe of RN functions is of increasing interest today: bacterial riboswitches: e.g. temperature sensing regulatory signals: e.g. iron responsive elements group 1 introns: self-splicing microrn and small interfering RN: translation supression tmrn: freeing stalled ribosomes from incomplete mrn RISPR RN: bacterial immune system and Lamarckian evolution and many 100s more... computer analogy: DN is the hard disk, RN the main memory. édric Saule

9 RN function: Some examples Depending on student background, let us discuss a few of the above RN functions (or some other ones) in some detail. édric Saule

10 RN chemistry RN is a chain molecule built from nucleosides, with a backbone of alternating ribose and phosphate groups. édric Saule

11 The four bases used in RN: édric Saule

12 RN (tertiary) structure n RN molecule folds back onto itself, forming helices and loops. RN helices are extremely stiff, exposing loops in welldefined positions. omputational challenge: Recognize signals from structure ND sequence. The structure itself is not uniquely defined, but must be seen as a Boltzmann ensemble, governed by free energy. RN 3D structure is difficult to resolve; two known examples are trn and group 1 introns édric Saule

13 Structure of a trn: édric Saule

14 Structure of a group 1 intron: édric Saule

15 Forces of structure formation: Hydrogen bonds between bases standard base pairs: Watson-rick,, and wobble non-standard base pairs almost any other base pair stacking, i.e. helix formation helix continuation ( dangling bases ) Negative (destabilizing) forces from loops Influence of Na+, K+ Mg+ (help to bend negative backbone) coaxial stacking of helices triple and quadruple helices édric Saule

16 Structural stability: Stability is measured in free energy Free energy is measured experimentally by melting temperature Energy contributions of local configurations have been determined experimentally édric Saule

17 look at the present energy parameters: See http: //rna.urmc.rochester.edu/nndb/turner04/index.1.html édric Saule

18 The folding process RN folds in an hierarchic fashion (Tinoco and Bustamente, 1999): 1 Local helices form, helped by metal ions 2 Local folding brings remote parts to vicinity; more helices form 3 Helices arrange themselves in 3D 4 Loops in distant helices may form long-distance base pairs and additional interactions (pseudo-knots) of increasing complexity 5 The process is reversible a folded structure may reshape with a certain probability There are also conformational switches, triggered by external events (sensors, thermometers) édric Saule

19 o-transcriptional folding Folding begins immediately when the RN is transcribed Molecule may be trapped in a non-optimal state fter heating and refolding the complete molecule, the native structure may not be recovered The folding path is engineered to avoid traps (cf. Meyer I.M., Miklos I. o-transcriptional folding is encoded within RN genes. BM Mol Biol ug 6;5(1):10) Some RN viruses have different structure before and after replication. édric Saule

20 RN 2D structure RN secondary structure is the level of base pairing and helices. The secondary structure strongly determines 3D structure (Parisien and Major, 2008) can be used to detect conservation of structure gives hints (only) to explore biochemical function can be computed by DP algorithms has become an accepted substitute for 3D structure édric Saule

21 Elements of secondary structure Multiple Loop Stacking Region Hairpin Loop Internal Loop Bulge Loop (left) Bulge Loop (right) édric Saule

22 bstraction (versus heuristic) RN secondary structure abstracts from 3D coordinates of atoms non-standard base pairs long-distance interactions coaxial stacking, triple and quadruple helices Secondary structure approximates phases 1 and 2 of hierarchical folding It is not a heuristic substitute for 3D structure édric Saule

23 omputational structure analysis: ll computational approaches concentrate on 2D structure. Some consider pseudo-knots, but most do not. lgorithms are available for Prediction of optimal or near-optimal structure(s) omputing free energy of a given structure omputing simarity/distances between structures Finding local similarities in structures ligning two or more structures Predicting consensus structure(s) from multiple sequences Simulating the kinetics of folding Predicting possibility of conformational switching and many more... édric Saule

24 Preview Next weeks session: Structure representations Structure prediction via base pair maximization édric Saule