Showing papers in "Annual Review of Biochemistry in 1993"

Signaling by Receptor Tyrosine Kinases

Abstract: This is a free sample of content from Signaling by Receptor Tyrosine Kinases Click here for more information or to buy the book. This is a free sample of content from Signaling by Receptor Tyrosine Kinases Click here for more information or to buy the book. Front cover artwork: Stylized representations of the 20 different receptor tyrosine kinase (RTK) families found in humans—accounting for a total of 58 different receptors. The common intra-cellular tyrosine kinase domain (lower part of each receptor) is shown as a red rectangle. Domains in the extracellular region (upper part of each receptor) are much more variable across families and include immunoglobulin domains (blue), fibronectin type III domains (orange), and many others. The chapters in this volume describe mechanisms by which ligand binding to the extracellular region controls activity of the intracellular kinase domain, which vary substantially across the family and drive a variety of intracellular signaling pathways. All World Wide Web addresses are accurate to the best of our knowledge at the time of printing. Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Cold Spring Harbor Laboratory Press, provided that the appropriate fee is paid directly to the Copyright Clearance Center (CCC). Write or call CCC at 222 Rosewood Drive, Danvers, MA 01923 (978-750-8400) for information about fees and regulations. Prior to photocopying items for educational classroom use, contact CCC at the above address. Additional information on CCC can be obtained at CCC Online at www.copyright.com.

Molecular chaperone functions of heat-shock proteins

Abstract: 3. HSP70 PROTEINS: CHAPERONES WITH DIVERSE ROLES IN PROTEIN METABOLISM . . .. . . . . . . . . .. . . . . .. . . ... . . . .... . . . . 357 Structure and Function of Hsp70 Chaperones . . . . . . . . . . . . . . . . . . . . . . . 357 Maintenance of the Translocation-Competent State of Precursor Proteins . . . . . . 359 The Hsp70 DnaK and Dna! are a Chaperone Team . . . . . . . . . . . . . . . . . . . 360 Organellar Hsp70s in Membrane Translocation and Folding .. . . . .. . . . . . . 361 Hsp70 in Cells Under Metabolic Stress . . . . . . . . . . . . . . . . . . . . . . . . . . . 362 Hsp70 and Protein Degradation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363

Biological Nitrogen Fixation

Abstract: Biological nitrogen fixation (BNF) is the process of the reduction of dinitrogen from the air to ammonia carried out by a large number of species of free-living and symbiotic microbes called diazotrophs. BNF presents an inexpensive and environmentally sound, sustainable approach to crop production and constitutes one of the most important Plant Growth Promotion (PGP) scenarios. Here I will summarize various aspects of BNF, including the dinitrogen reduction catalysed reaction carried out by “nitrogenase” and the enzymes/genes involved and their regulation, the inherent “oxygen paradox” , the identification of diazotrophs, sustainable agricultural uses of BNF, symbiotic plant-diazotroph interactions and endophytic diazotrophs, data from the field, and future prospects in BNF.

hnRNP Proteins and the Biogenesis of mRNA

Abstract: II. THE hnRNP PROTEINS . Definition and Experimental Criteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . Human . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Other Organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Posttranslational Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Oxidation of free amino acids and amino acid residues in proteins by radiolysis and by metal-catalyzed reactions

Abstract: Basic mechanisms that underlie the oxygen free radical-promoted oxidation of free amino acids and amino acid residues of proteins are derived from radiolysis studies. Results of these studies indicate that the most common pathway for the oxidation of simple aliphatic amino acids involves the hydroxyl radical-mediated abstraction of a hydrogen atom to form a carbon-centered radical at the alpha-position of the amino acid or amino acid residue in the polypeptide chain. Addition of O2 to the carbon-centered radicals leads to formation of peroxy radical derivatives, which upon decomposition lead to production of NH3 and alpha-ketoacids, or to production of NH3, CO2, and aldehydes or carboxylic acids containing one less carbon atom. As the number of carbon atoms in the amino acid is increased, hydrogen abstraction at other positions in the carbon chain becomes more important and leads either to the formation of hydroxy derivatives, or to amino acid cross-linked products as a consequence of carbon-centered radical recombination processes. alpha-Hydrogen abstraction plays a minor role in the oxidation of aromatic amino acids by radiolysis. Instead, the aromatic ring is the primary site of attack leading to hydroxy derivatives, to ring scission, and in the case of tyrosine to the formation of Tyr-Tyr cross-linked dimers. The basic pattern for the oxidation of amino acids by metal ion-catalyzed reactions (Fenton chemistry) is similar to the alpha-hydrogen abstraction pathway. But unlike the case of oxidation by radiolysis, this Fenton pathway is the major mechanism for the oxidation of all aliphatic amino acids, regardless of chain length, as well as for the oxidation of aromatic amino acids. Curiously, the Fe(III)-catalyzed oxidation of free amino acids is almost completely dependent upon the presence of bicarbonate ion, and is greatly stimulated by iron chelators at chelator/Fe(III) ratios less than 1.0, and is inhibited at chelator/Fe(III) ratios greater than 1.0. It is deduced that the most active catalytic complex is composed of two equivalents of HCO3-, an amino acid, and at least one equivalent of iron; however, two forms of iron, an iron-chelate and another form, must somehow be involved. In contrast to the situation with radiolysis, the aromatic rings of aromatic amino acids are only minor targets for metal-catalyzed reactions. All amino acid residues in proteins are subject to attack by hydroxyl radicals generated by ionizing radiation; however, the aromatic amino acids and sulfur-containing amino acids are most sensitive to oxidation.(ABSTRACT TRUNCATED AT 400 WORDS)

Structure-based inhibitors of hiv-1 protease

Abstract: INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 544 HIV-l PROTEASE STRUCTURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 545 Description of the HIV-J PR Molecule ....... .... .. . ... 546 Symmetry of the Enzyme and Its Crystallographic Manifestation . . . . . . . . . . . 549 Substrate Specificity of HIV PR . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . 554 SUBSTRATE-ANALOG INHIBITOR DESIGN ......... . 555 INHIBITOR COMPLEXES OF HIV-l PR . . . . . . . . . . . . . . . . . . . . . . . . . . . 558 Common Structural Features . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . 559 Subsites and Subsite-Inhibitor Interactions . . . . . . . . . . . . . . . . . . . . . . . . . 561 Transition-State Inhibitor Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566 STRUCTURE-BASED INHIBITOR DESIGN . . . . . . . . . . . . . . . . . . . . . . . . . 573 Use of Structure for New Lead Discovery . . . . . . . ... . . .. . . . ... . . ... 575 SCREENING AND SERENDIPITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 577 SUMMARY AND CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579 Is Symmetry Important in Inhibitor Design? . . . . . . . . . . . . . . . . . . . . . . . . 579 Subsitellnhibitor Contacts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579 Conclusions .... . . .. . 580

Membrane-Anchored Growth Factors

Abstract: STRUCTURE AND BIOLOGY OF MEMBRANE-ANCHORED GROWTH FACTORS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1 6 The EGF Family . . . . . . . . . . . . . . . ... .. . . . ... ... . .. . ... . . . . 5 1 8 Colony-Stimulating Factor-] . . . . . .... . . . .... . . . . . . . . . . . .. . . . . 524 Kit Ligand . . . .. . .. . . . .. . . .. . . ... . . . . . . .. . . . . . . . . .. . . . . 525 Tumor Necrosis Factor-a. ... . . . ... ... .. . . . . . . ... . . . .... . . . .. 525 The Bride oj Sevenless Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526 UNIQUE BIOLOGICAL ROLES OF MEMBRANE-ANCHORED GROWTH FACTORS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527 Cell-Cell Contacts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 528 Juxracrine Stimulation .... . . ... . . . . . . .. .. . ... . . . ... . . . . . ... 528 Soluble Forms May Not SubstituteJor Membrane-Anchored Forms. . . . . . . . . . 529 Membrane Growth Factors as Receptors. . . . . . . . . . . . . . . . . . . . . . . . . . 529 Endocytosis of a Membrane-Anchored Ligand. . . . . . . . . . . . . . . . . . . . . . . 530 RELEASE OF MEMBRANE-ANCHORED GROWTH FACTORS . . . . . . . . . . . . 530 Cellular Location and Specificity of the Cleavage Process .. . . . .. . . . . ... 531 Alternative Splicing of Cleavage Regions. . . . . . . . . . . . . . . . . . . . . . . . . . 533 Regulation of Cleavage . . . . .. ... ... . . . ... . . . .. . . .. .... . . . . . 534 Determinants of Membrane Growth Factor Cleavage . . ... . . . .... ... . . . 536

Conformational Coupling in DNA Polymerase Fidelity

Abstract: The fidelity of DNA polymerases is largely attributable to a two-step nucleotide binding mechanism. In the first step, binding contacts are initially made between the template and the incoming dNTP. The selectivity of this ground-state binding is similar in magnitude to the selectivity seen in forming base pairs in solution. In the second step, a change in protein conformation occurs, which leads to rapid incorporation of the dNTP into the growing polymer. This conformational change appears to occur globally in that it is inhibited by mismatches in the dNTP or in any of the three terminal base pairs of the primer/template. The open conformation allows rapid binding of the dNTP from solution, while the closed conformation provides steric checks for the proper Watson-Crick base pair geometry. This conformational change accounts for the extraordinary fidelity of polymerization and also provides selectivity to the exonuclease by inhibiting polymerization over a mismatch in the primer/template. The overall fidelity approaches one error in 10(10) by a combination of selectivity in polymerization (10(5)-10(6)) and in proofreading (10(3)-10(4)). This paradigm provides the theoretical basis for further investigation of the structural basis for fidelity by pointing to the essential elements of the polymerization reaction that need to be examined in order to evaluate active-site-directed mutants of polymerases to test appropriate structure/function relationships.

The Structure and Biosynthesis of Glycosyl Phosphatidylinositol Protein Anchors

Abstract: GPI STRUCTURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 ATTACHMENT OF THE GPI TO PROTEIN . . . . . . . . . . . . . . . . . . . . . . . . . 126 The Anchor Precursor . _ . . . _ _ . . . . . . . . . . . . . . . . . 126 Sequence Determinants Jor Anchor Addition. . . . . . . . . . . . . . . . . . . . . . . . 127 The Mechanism oj Anchor Addition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 GPI BIOSYNTHESIS . . .... . . . . . . . . ........ . . . . . . . . .. .... . . 129 Synthesis oJ Glucosaminyl-Phosphatidylinositol . . . . . . . . . . . . . . . . . . . . . . 130 Addition oj Mannose .. . ... .... . . . . ... . ... .. .... . . . . .. . . .. 130 Addition oj Phosphoethanolamine .. ..... . . . . .. . .. . . 131 GPls with Acylated Inositols . . . .... . . . . . . . . . . ..... .... ..... . . 131 Unique Features oJ GPI Biosynthesis in Mammalian Cells . . . . . . . . . . . . . . . 131 Intracellular Location oJ GPI Biosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . 132 GPI Remodeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Mammalian Cells Defective in GPI Biosynthesis . . . ........ . .. ..... 134 THE FUTURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

Protein Tyrosine Phosphatases

Abstract: The process of reversible phosphorylation is perhaps the cell's most prevalent means of regulation at the molecular level. It has been estimated that up to 30% of all cellular proteins are phosphorylated, and phosphorylation has been shown to play a crucial regulatory role in such diverse cellular events as metabolism, growth and differentiation, vesicular transport, and gene transcription. Phosphorylation and dephosphorylation are carried out by kinases and phosphatases, respectively. There are currently predicted to be 518 kinases and ~125 phosphatases encoded in the human genome, further underscoring the overall importance of phosphorylation in molecular regulation. Phosphatases are generally divided into two main families based on their catalytic mechanism and substrate specificity: the protein phosphatases (PPs), which exclusively desphosphorylate serine and threonine residues, and the protein tyrosine phosphatases (PTPs), which can dephosphorylate tyrosine residues, and are the focus of this article. PTPs can be further classified into subfamilies based on (1) subcellular location (receptor vs. intracellular), (2) substrate preference, and (3) three-dimensional topology. In this article, we describe the different subfamilies of PTPs and their conserved catalytic mechanism. In addition, we briefly discuss human diseases that result from disrupted PTP signaling, and discuss the pursuit of PTPs as drug targets.

The Tumor Suppressor Genes

Abstract: THE ORIGINS OF THE CONCEPT OF TUMOR SUPPRESSOR GENES . . . . . . . 623 THE PROPERTIES OF ONCOGENES AND TUMOR SUPPRESSOR GENES . . 627 THE ONCOGENES OF THE DNA TUMOR VIRUSES TARGET THE MAJOR CELLULAR TUMOR SUPPRESSOR GENES 629 THE RETINOBLASTOMA SUSCEPTIBILITY GENE AND PROTEIN ........ 632 THE RB-RELATED PROTEIN, pI07 635 THE p53 GENE AND PROTEIN 636 THE WILMS' TUMOR GENE AND PROTEIN . . . . . . . . . . . . . . . . . . . . . . . 644 THE NEUROFIBROMA TOSIS-1 GENE AND PROTEIN . . . . . . . . . . . . . . . . . 645 ADENOMATOUS POLYPOSIS COLI (APC) GENE AND ITS PROTEIN ...... 646 DELETED IN COLORECTAL CANCER; THE DCC GENE AND PROTEIN . . . . . 646

New Photolabeling and Crosslinking Methods

Abstract: INTRODUCTION AND SUMMARY 483 PHOTOLABILE GROUPS AND REACTIVE INTERMEDIATES . . . . . . . . . . . . 485 Generators of Carbenes and Nitrenes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 486 Arylketones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489 Reagents for Target Site-Selective Activation . . . . . . . . . . . . . . . . . . . . . . . 489 PHOTOLABELlNG OF THE APOLAR CORE OF MEMBRANES . . . . . . . . . . . 490 Introductory Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 490 Design and Properties of Reagents .. . . ...... . . . . . ... . .. . . . . .... 491 General Features of Hydrophobic Photolabeling of Membranes. . . . . . . . . . . . 494 Hydrophobic Photolabeling of Integral Proteins . . . . . . . . . . . . . . . . . . . . . 496 Recent Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500 Photo-activatable Phospholipids as Photo-affinity Probes . . . . . . . . . . . . . . . . 502 APPROACHES TO "SITE-SPECIFIC" PHOTOCROSSLINKING . . . . . . . . . . . . 503 Synthetic Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503 Photo-activatable Proteins Through Modification of Reactive Amino Acid Residues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 505 Site-Directed, Biosynthetic Incorporation of Photo-activatable Amino Acids Into Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 506 CONCLUSIONS AND PROSPECTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 509

Structural and Genetic Analysis of Protein Stability

Abstract: One very encouraging development has been the freedom with which amino acid replacements can be introduced in a protein of interest. This has made it possible to obtain detailed structural and thermodynamic data on a wide variety of mutants that modify protein stability. Substitutions of solvent-exposed amino acids on the surfaces of proteins are seen to have little if any effect on protein stability or structure, leading to the view that it is the rigid parts of proteins that are critical for folding and stability. There is every reason to expect that it will be possible to rationalize the stabilities of mutant proteins from accurate knowledge of their structures. Substantial progress is being made in quantitating the interactions that determine and stabilize protein structures. Although not specifically the subject of this review, substantial progress is also being made in developing methods to engineer proteins of enhanced stability.

General Initiation Factors for RNA Polymerase II

Abstract: A WORKING MODEL FOR ASSEMBLY O F THE ACTIVE PREINITIA TION COMPLEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 THE INITIAL COMPLEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 63 Structure and Properties ofTATA Box-Binding Protein. . . . . . . . . . . . . . . . . 1 65 Structure and Properties of the Native TATA Factor . . . . . . . . . . . . . . . 166 TFIIA . .. . . . ... . . .. . . . . . . . . . . . . . . . . . .. . . . . .. . . . . . . ... 169 THE COMPLETE PREINITIATION COMPLEX . . . . . . . . . . . . . . . . . . . . . . . 170 Factors Involved in Assembly of the Complete Preinitiation Complex . . . . . . . . 170 Pathway(s) for Assembly of the Complete Preinitiation Complex . . . ..... . . . 176 Evidence for an RNA Polymerase II Holoenzyme. . . . . . . . . . . . . . . . . . . . . 179 ATP-DEPENDENT ACTIVATION OF THE COMPLETE PREINITIA TION COMPLEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 80 THE RNA POLYMERASE II C-TERMINAL DOMAIN . . . . . . . . . . . . . . . . . . 1 8 1 A Role for the C-Terminal Domain in Transcription Initiation . . . . . . . . . . . . . 1 8 1 Phu>phoryiation of the C-Terminal Domain . . . . . . . . . . . . . . . . . . . . . . . . 1 83

Pathways of protein folding

Abstract: Advances in spectroscopy, protein engineering, and peptide synthesis have had a dramatic impact on the understanding of the structures and stabilities of transient folding intermediates. The data available from a variety of proteins point to the existence of three common stages of folding. 1. Initially, the unfolded protein collapses to a presumably more compact form containing substantial nonpolar surfaces and secondary structure. This species has little thermodynamic stability and encompasses an ensemble of conformations that are in dynamic equilibrium and may contain non-native elements of structure. This reaction occurs in less than 5 ms and, from a thermodynamic perspective, may be a noncooperative transition. The relatively high content of secondary structure implies that this manifold of states must be far smaller than the manifold for the unfolded protein. 2. The next phase involves the further development of secondary and the beginnings of specific tertiary structure throughout the protein as well as of measurable stability. Nativelike elements of structure appear, possibly in the form of subdomains that are yet to be properly docked. In many instances, the packing is not as tight as is ultimately found in the native conformation, suggesting that the side chains are in general more mobile. Some elements of surface structure, such as loops and the peripheries of sheets and helices, are not yet well defined. This stage, which may consist of more than a single kinetic step, occurs in the 5-1000 ms time range. The ensemble of conformations is much reduced from the first stage; however, it is far from a single, highly populated form. 3. The final stage in folding corresponds to the concerted formation of many noncovalent interactions throughout the protein. The solidlike interior packing is achieved; the final secondary structure forms and the surface structures settle into place. The breadth of these conformational changes reflects the global cooperativity characteristic of protein folding reactions. A pictorial representation of the kinetic and thermodynamic aspects of this process is shown in Figure 1. This folding scheme emphasizes the progressive development of structure and stability through an ever-slowing set of reactions. Because the product of each stage of folding, with the exception of the final step, is an ensemble of related but not identical species, it is an oversimplification to describe the process as a pathway. Perhaps it is better described as a series of transitions between manifolds of structures that are in dynamic equilibrium within any given set.(ABSTRACT TRUNCATED AT 400 WORDS)

Eukaryotic DNA Replication: Anatomy of An Origin

Abstract: PERSPECTIVE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 ORIGINS OF DNA REPLICATION IN SIMPLE GENOMES . . . . . . . . . . . . . . . 31 Functional and Genetic Origins Are Coincident . . . . . . . . . . . . . . . . . . . . . 3 1 Basic Components of an Ori[?in of Replication 32 Mechanisms by Which Transcription Facton Facilitate Origin Activity ....... 38 Summary . .... . . ...... . . . . 44 ORIGINS OF DNA REPLICATION IN COMPLEX GENOMES . . . . . . . . . . . . . 44 Replication Structures Appear Throughout a Broad Initiation Zone . . . . . . . . . . 44 Most Replication Events Begin Within a Small DNA Locus . . . . . . . . . . . . . . . 46 Replication Forks are Initiated at a Specific Site Within the Initiation Zone . . .. 48 Composition of Mammalian Origins of Bidirectional Replication . . ......... 49

Membrane Partitioning During Cell Division

Abstract: INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323 MORPHOLOGICAL CHANGES ... 324 Nuclear Envelope and Rough Endoplasmic Reticulum . . . . . . . . . . . . . . . . . . 326 Golgi Apparatus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327 Other Organelles . . . . . . . . . . . . . . . . .. . . . . . . . .. . . . . . . . . . . . . . 329 MEMBRANE TRAFFIC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329 Endocytosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329 Exocytosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331 Membrane Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333 MECHANISM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333 Fragmentation of the Nuclear Envelope and Golgi Apparatus . . . . . . . . . . .. . 334 Fragmentation in Interphase Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336 Vesiculation of the Golgi Apparatus and Nuclear Envelope . . . . . . . . . . . . . . 336 Reassembly of the Nuclear Envelope and Golgi Apparatus . . . . . . . . . . . . . . . 338 Role of Microtubules in Membrane Partitioning . . . . . . . . . . . . . . . . . . . . . 339 PARTITIONING ACCURACY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339 Strategies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339 Positioning of the Cleavage Furrow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342 Budding Yeast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342 Physiological Need for Partitioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343 SUMMARY AND FUTURE PROSPECTS . ........ . ... ......... .... 343

Control of Transcription Termination by RNA-Binding Proteins

Abstract: TRANSCRIPTION ME CHANI SMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 895 RNA Polymerase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 895 Trans�ripti�n. I,!itiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 896 AbortIve ImttatlOn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 897 The Inchworm Model of Transcript Elongation . . . . . . . . . . . . . . . . . . . . . . 897 The Elongation-Termination Decision . . . . . . . . . . . . . . . . . . . . . . . . . . . . 899 A Novel Mechanism of Termination in Plasmid ColEI . . . . .. . . . . . . . . . . . 902 Transcription Arrest and Resumption of Elongation by Transcript Cleavage . . . . 902 CONTROL OF TRANSCRIPTION TERMINATION . . . . . . . . . . . . . . . . . ... 904 Factors Inducing Intrinsic Termination . . . . . . . . . . . . . . . . . . . . . . . . . . . 904 E . coli Rho Protein: A Global Termination Factor . . . ... . . . ... . ..... . 904 E. coli BglG Protein: A Suppressor of Intrinsic Termination . . . . . . . . . . . . . . 907 Suppressors of Rho-Dependent Termination . . . . . . . . . . . . . . . . . . . . . . . . 908 Phage}.. N and Q Proteins: Antiterminators That Alter RNAP . . . . . . . . . . . . . 908 Phage HK022 Nun Protein: A Factor With Reversible Functions? .. . . . . . . . . 9 1 8 HIV Tat Protein: A Transcription Processivity Factor . . . . . . . . . . . . . . . . . . 919

Cytoplasmic Microtubule-Associated Motors

Abstract: THE KINESTNS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433 Identification and Structure . . . . .... . . . . ... . . .. . . .. ..... . ... . . 433 Mechl1:noc�em!stry and Force Generation ... . 436 FunctIOns In VIVO • . . . • . . . • . . . • . . . • . . . • . . . • . . . • . . . • . . . . . . . 440 CYTOPLASMIC DYNEIN . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . 443 Identification and Structure .. . ... . . .. . . .. . ... . . . . . . ... . . . . . . . 443 Mechanochemistry and Force Generation . .. . .. . ....... . . . . . . .... . 444 Functions in vivo . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . 446

The Receptors For Nerve Growth Factor and Other Neurotrophins

Abstract: OVERVIEW .. . . . . . . . . . .. . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 823 HISTORICAL ASPECTS . . . . . . . .. . . . . . . . . .. . . . . . . . . . .. . . . . . . . 825 MOLECULAR PROPERTIES . . . . . . . . . . . . . . . . ... . . . . .. . . .... . . . 827 Low-Molecular-Weight Receptor (LNGFR; p75) . l.:' . • . . . . . . . . . . . . • . . . 827 High-Molecular-Weight Receptor (HNGFR; p14(/"1r ;TrkA) . . . . . . . ... . . . . 831 Models for the Biologically Active Receptor . . . . . . . . . . . . . . . . . . . . . . . . 833 Other Neurotrophic Receptors . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . 835 Nuclear Receptorsfor NGF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 837 DISTRIBUTION AND EXPRESSION . . . . . . . .. . . . . . . . . . ... . .. . . . . . 837 Neuronal Tissues . . .. . . . . .. . . . . . . . . . . . . . . .... . . . . . ... . . . . 837 Non-neuronal Tissues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 839 Tumor Cell Lines . . . . .. . . . . . . . . . . . . . . .. . . . . . . . .. . . . . . . . . . 840 FUNCTIONAL CHARACTERISTICS . . . . . ... . . . . . . . . . . . . . . . . . . . . . 841 Tyrosine Phosphorylation 841 Signal Transduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 843

Determination of RNA structure and thermodynamics

Abstract: PHYLOGENETIC AND MUTATIONAL ANALYSES . . . . . . . . . . . . . . . . . . . 258 Natural Sequence Variability 258 Artificial Phylogeny . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259 Random Mutations and Specific Selection . .... . . . . . . ... . .. . . . . . . . . 260 Functional Group Mutations .. . . . .. . . . . . .. . . . .. . . . .. . .... . . . . 260 OPTICAL SPECTROSCOPY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260 Absorbance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260 Circular Dichroism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263 Fluorescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263

Nucleocytoplasmic transport in the yeast Saccharomyces cerevisiae.

Abstract: INTRODUCTION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219 GENERAL FEATURES OF MOVEMENT OF PROTEINS AND RNA BETWEEN THE NUCLEUS AND CYTOPLASM. . . . . . . . . . . . . . . . . . . . . . . 220 Entry of Proteins into the Nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220 Export of RNA from the Nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222 COMPOSITION AND DYNAMICS OF THE YEAST NUCLEAR ENVELOPE ... 222 Structure of the Yeast Nucleus . . ...... . . . . . . . .. . . . . ...... ..... 222 Behavior of the Nuclear Envelope During Mitosis in Yeast. . . . . . . . . . . . . . . 227 Nuclear Pore Complexes in Yeast . .. . . .. . . . .. . . ... . . ..... . ..... 228 RECOGNITION OF PROTEINS FOR IMPORT INTO THE YEAST NUCLEUS . . . 232 Nuclear Localization Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232 In vitro Studies of Nuclear Transport with Yeast ..... . . . 237 Yeast Proteins that Bind Nuclear Localization Sequences. . . . . . . . . . . . . . . . 239 IN VIVO STUDIES OF NUCLEAR TRANSPORT 241 Nuclear Protein Localization Mutants. . . . . . . . . . . . . . . . . . . . . . . . . . . . 241 RNA Export Mutants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243 REGULATION OF NUCLEAR PROTEIN UPTAKE 245 Swi5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245 Ace2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246 Cdc46 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246 Glucocorticoid Receptor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248

From Bacterial Nutrition to Enzyme Structure: A Personal Odyssey

Abstract: As a former editor or member of the Editorial Board of the Annual Review of Biochemistry I helped to select authors of the prefatory chapters for more than 20 years. Now I am asked to write one myself. The first such chapter appeared in 1953 with the prefatorial statement: “This is the first of a series in which it is the hope of the Editorial Committee that our elders in biochemistry will give us through chapters of a historical and philosophical character the benefit of their long years of experience in biochemistry.” With one exception, the chapters have appeared regularly ever since. Their authors comprise a group I am proud to join even while harboring some doubts about really belonging. Their autobiographical accounts have added much to our understanding of how and why they became biochemists, and how biochemistry itself developed. I shall continue in this tradition.