1. Introduction 222

2. What is an RNA motif? 222

2.1 Sequence vs. structural motifs 222

2.2 RNA structural motifs 223

2.3 RNA structural elements vs. motifs 223

2.4 Specific recognition motifs 224

2.5 Tools for identifying and classifying elements and motifs 226

3. Types of RNA structural motifs 228

3.1 Helices 228

3.2 Hairpin loops 228

3.3 Internal loops 230

3.4 Junction loops/multiloops 230

3.5 Binding motifs 232

3.5.1 Metal binding 232

3.5.2 Natural and selected aptamers 234

3.6 Tertiary interactions 234

4. Future directions 236

5. Acknowledgments 239

6. References 239

RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common ‘structural elements’. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.

1. Introduction 2

2. The macroscopic and microscopic views of protein folding 2

2.1 The macroscopic view: the experimental folding free-energy profile 2

2.2 The microscopic view: an underlying energy landscape 3

3. The micro to macro projection: from an energy landscape to a free-energy profile 6

4. Global features of the protein folding transition-state ensemble 12

4.1 Overall transition state location β[Dagger]: a measure of compactness 12

4.2 What makes folding so robust ? 13

5. Structural characterization of the transition-state ensemble 16

5.1 Insights from ϕ-value analysis 16

6. Deviations from ideality 20

6.1 β[Dagger] shifts along seemingly robust trajectories 21

6.2 Anomalous ϕ values, frustration and inhomogeneities 25

7. Intermediates 28

8. Detours, traps and frustration 29

8.1 Premature collapse and non-native trapping 29

9. Diffusion on the energy landscape and the elementary events of protein folding 30

10. Malleability of folding routes: changes of the dominant collective coordinates for folding 33

11. The evolution of the shape of the energy landscape 35

11.1 Negative design: the hidden dimension of the folding code 35

12. Mechanistic multiplicity and evolutionary choice 36

13. Acknowledgements 37

14. References 38

We review what has been learned about the protein-folding problem from experimental kinetic studies. These studies reveal patterns of both great richness and surprising simplicity. The patterns can be interpreted in terms of proteins possessing an energy landscape which is largely, but not completely, funnel-like. Issues such as speed limitations of folding, the robustness of folding, the origin of barriers and cooperativity and the ensemble nature of transition states, intermediate and traps are assessed using the results from several experimental groups highlighting energy-landscape ideas as an interpretive framework.