Folding and self-assembly of biological macromolecules : proceedings of the Deuxiémes Entretiens de Bures : Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette, France, 27 November-1 December 2001

This proceedings volume explores the pathways and mechanisms by which constituent residues interact and fold to yield native biological macromolecules (catalytic RNA and functional proteins), how ribosomes and other macromolecular complexes self-assemble, and relevant energetics considerations. At the week-long interactive conference, some 20 leading researchers reported their most pertinent results, confronting each other and an audience of more than 150 specialists from a wide range of scientific disciplines, including structural and molecular biology, biophysics, computer science, mathematics, and theoretical physics. The fourteen papers — and audience interaction — are edited and illustrated versions of the transcribed oral presentations. Organizers and Speakers......Page 6 Editor's Note......Page 8 Preface......Page 10 CONTENTS......Page 16 Evolution-Based Genome Analysis: An Alternative to Analyze Folding and Function in Proteins......Page 18 Why is DNA the way it is?......Page 21 Conformation of Charged Polymers: Polyelectrolytes and Polyampholytes......Page 60 Statistically Derived Rules for RNA Folding......Page 90 Experimental Approaches to RNA Folding......Page 116 Summary......Page 140 References......Page 142 Some Questions Concerning RNA Folding......Page 144 References......Page 194 RNA Folding in Ribosome Assembly......Page 196 From RNA Sequences to Folding Pathways and Structures: A Perspective......Page 228 An Evolutionary Perspective on the Determinants of Protein Function and Assembly......Page 242 The evolutionary trace method......Page 243 Basic control studies......Page 248 G protein signaling......Page 250 Regulators of G protein signaling......Page 252 Applications to functional annotation......Page 254 G protein-coupled receptors......Page 258 Proteome-scale ET......Page 262 Specific applications......Page 269 Introduction......Page 272 Identifying invariant structural characteristics in a group of non-homologous sandwich-like proteins......Page 275 Identification of SP sequence determinants......Page 276 Using sequence determinants to classify proteins: an illustration......Page 280 Discussion......Page 282 References......Page 283 Structure-Function Relationships in Polymerases......Page 284 1. Classification of polymerases by sequence analysis......Page 287 2. Structure-function relationship in a template-independent DNA polymerase......Page 296 3. Normal mode analysis of the open-to-closed transition......Page 308 4. Electrostatics and translocation......Page 314 The protein folding problem......Page 320 The folding nucleus......Page 323 Lattice proteins......Page 324 The folding process......Page 329 Universally conserved folding nuclei......Page 336 Introduction......Page 340 Discovery of GroEL......Page 341 Spontaneous folding mechanisms......Page 345 Dissecting problems associated with assisted folding......Page 348 Virus Assembly and Maturation......Page 366 Properties of a virus infection......Page 367 Viral subunit functions......Page 368 Icosahedral symmetry......Page 370 Quasi-equivalent virus capsids......Page 372 Cowpea Chlorotic Mottle Virus (CCMV) assembly......Page 373 Assembly of nodaviruses......Page 377 Assembly of tetraviruses......Page 382 Assembly of HK97 a double-strand DNA bacteriophage......Page 385 The Animal in the Machine: Is There a Geometric Program in the Genetic Program?......Page 392 Cells as Turing machines......Page 393 Different levels of information......Page 395 DNA management......Page 399 To lead or to lag?......Page 402 From function to structure......Page 406 What does my neighbor tell me?......Page 411 Organized by Alessandra Carbone (IHÉS, Bures-sur-Yvette, France) Organized by Misha Gromov (IHÉS, Bures-sur-Yvette, France) Organized by François Képès (CNRS-Genopole