RNA Protein Interaction

Transcription

1 Introduction RN binding in detail structural analysis Examples RN Protein Interaction xel Wintsche February 16, 2009 xel Wintsche RN Protein Interaction

2 Introduction RN binding in detail structural analysis Examples Table of ontents 1 Introduction 2 RN binding in detail 3 structural analysis of local contexts of consensus sequences 4 Examples xel Wintsche RN Protein Interaction

3 Introduction RN binding in detail structural analysis Examples Introduction RN is more than an intermediate step in protein expression not every RN is translated (ncrns) RN can be linked with regulatory processes in cell TRs of some mrns have conserved regions carry information important for fitness xel Wintsche RN Protein Interaction

4 Introduction RN binding in detail structural analysis Examples Introduction one way to participate in regulatory mechanisms is to bind to a protein can induce conformational changes and results in new functionality RN-protein binding leads to direct regulation of the RN (translational repression of mrn) understanding of RN-protein binding is important to understand many regulatory processes xel Wintsche RN Protein Interaction

5 Introduction RN binding in detail structural analysis Examples Introduction one way to participate in regulatory mechanisms is to bind to a protein can induce conformational changes and results in new functionality RN-protein binding leads to direct regulation of the RN (translational repression of mrn) understanding of RN-protein binding is important to understand many regulatory processes prediction of RN-protein interaction is hard to compute xel Wintsche RN Protein Interaction

6 Introduction RN binding in detail structural analysis Examples Introduction How recognise proteins their RN targets? Is RN sequence and/or RN structure important for specific binding? xel Wintsche RN Protein Interaction

7 Introduction RN binding in detail structural analysis Examples Two Examples of RN binding protein domains RRM: RN Recognition Motif The information of structure, RN binding and pictures are taken from [4] and [1] KH: K Homology Domain The information of structure, RN binding and pictures are taken from [5] and [2] xel Wintsche RN Protein Interaction

8 Introduction RN binding in detail structural analysis Examples RN Recognition Motif RRM can be found in all eukaryotic organisms one of the most widely spread domains in eukaryots (H. sapiens has at least 497 proteins) often more than one RRM per protein identified in the 80s while investigating mrn precursors RRM is part of many different functions in cell xel Wintsche RN Protein Interaction

9 Introduction RN binding in detail structural analysis Examples RN Recognition Motif RRM has a length of about 90 it folds into an αβ sandwich (β 1 α 1 β 2 β 3 α 2 β 4 ) spacially arranged in one four-stranded antiparallel β-sheet (β 4 β 1 β 3 β 2 ) xel Wintsche RN Protein Interaction

10 Introduction RN binding in detail structural analysis Examples RN Recognition Motif RN binds mainly to the β-sheet 5 end is located on β 4 β 1, 3 end on β 3 β 2 sequence specifity by sidechain interaction β-sheet detects only a dinucleotide xel Wintsche RN Protein Interaction

11 Introduction RN binding in detail structural analysis Examples RN Recognition Motif additional RRMs allow recognition of longer sequences xel Wintsche RN Protein Interaction

12 Introduction RN binding in detail structural analysis Examples RN Recognition Motif additional RRMs allow recognition of longer sequences RRM of 1 needs secondary RN structure to bind (stem loop or internal loop) xel Wintsche RN Protein Interaction

13 Introduction RN binding in detail structural analysis Examples K homology domain first discovered in K-proteins (human hnrnp) KH is a common and widespread domain KH exists in all three kingdoms and hence arose early in evolution most KH-proteins have more than one KH domain xel Wintsche RN Protein Interaction

14 Introduction RN binding in detail structural analysis Examples K homology domain KH has a length of about 70 fold into β 1 α 1 α 2 β 2 β 3 α 3 spacially forming a β 1 β 3 β 2 -sheet xel Wintsche RN Protein Interaction

15 Introduction RN binding in detail structural analysis Examples K homology domain KH has a length of about 70 fold into β 1 α 1 α 2 β 2 β 3 α 3 spacially forming a β 1 β 3 β 2 -sheet binds RN in a different manner to RRM, suggesting that the structural convergence of RN binding proteins has little to do with RN recognition xel Wintsche RN Protein Interaction

16 Introduction RN binding in detail structural analysis Examples Materials and Software Materials Proteins and related RN consensus sequences [3] yeast genome from enbank yeast mrn annotations from enbank xel Wintsche RN Protein Interaction

17 Introduction RN binding in detail structural analysis Examples Materials and Software Materials Proteins and related RN consensus sequences [3] yeast genome from enbank yeast mrn annotations from enbank Software pwmatch: find sequence matches in a genome (treshold parameter 1 = exact match) RNfold: predict RN secondary structure xel Wintsche RN Protein Interaction

18 Introduction RN binding in detail structural analysis Examples first simple approach 1 translate rna consenus sequence into PWM 2 search matches on genome with pwmatch 3 select matches laying in annotated mrns 4 cut out matches plus offset 5 fold sequences with RNfold xel Wintsche RN Protein Interaction

19 Introduction RN binding in detail structural analysis Examples first simple approach 1 translate rna consenus sequence into PWM 2 search matches on genome with pwmatch 3 select matches laying in annotated mrns 4 cut out matches plus offset 5 fold sequences with RNfold Example of consensus sequnece to PWM conversion HNBWH : : : : xel Wintsche RN Protein Interaction

20 Introduction RN binding in detail structural analysis Examples Example Proteins SP160 function: involved in the control of mitotic chromosome transmission contains 7 KH domains RN consensus sequence: xel Wintsche RN Protein Interaction

21 Introduction RN binding in detail structural analysis Examples Example Proteins SP160 function: involved in the control of mitotic chromosome transmission contains 7 KH domains RN consensus sequence: PIN4 function: involved in normal 2/M phase transition of the mitotic cell cycle contains 1 RRM domain RN consensus sequence: KWYBN xel Wintsche RN Protein Interaction

22 Introduction RN binding in detail structural analysis Examples Examples SP160 xel Wintsche RN Protein Interaction

23 Introduction RN binding in detail structural analysis Examples Examples SP160 xel Wintsche RN Protein Interaction

24 Introduction RN binding in detail structural analysis Examples Examples SP160 xel Wintsche RN Protein Interaction

25 Introduction RN binding in detail structural analysis Examples Examples PIN4 xel Wintsche RN Protein Interaction

26 Introduction RN binding in detail structural analysis Examples Examples PIN4 xel Wintsche RN Protein Interaction

27 Introduction RN binding in detail structural analysis Examples Examples PIN4 xel Wintsche RN Protein Interaction

28 Introduction RN binding in detail structural analysis Examples Literature. léry, M. Blatter, and F.H.T. llain. RN recognition motifs: boring? Not quite. urrent Opinion in Structural Biology, 18(3): , N.V. rishin. KH domain: one motif, two folds. Nucleic cids Research, 29(3): , D.J. Hogan, D.P. Riordan,.P. erber, D. Herschlag, and P.O. Brown. Diverse RN-Binding Proteins Interact with Functionally Related Sets of RNs, Suggesting an Extensive Regulatory System. PLoS Biol, 6(10):e255, Maris,. Dominguez, and F.H.T. llain. The RN recognition motif, a plastic RN-binding platform to regulate post-transcriptional gene expression. FEBS Journal, 272(9): , J.M. Pérez-añadillas and. Varani. Recent advances in RN protein recognition. urrent Opinion in Structural Biology, 11(1):53 58, xel Wintsche RN Protein Interaction

29 Introduction RN binding in detail structural analysis Examples Thank you for listening! xel Wintsche RN Protein Interaction