Progress in Nucleic Acid Research and Molecular Biology (eBook)

Kivie Moldave (Herausgeber)

eBook Download: PDF | EPUB

1998 | 1. Auflage
373 Seiten
Elsevier Science (Verlag)
978-0-08-086347-4 (ISBN)

Infos

Key Features
* Provides a forum for discussion of new discoveries, approaches, and ideas in molecular biology
* Contributions from leaders in their fields
* Abundant references

Inhalt

Cover 
1 
Contents 
6 
Some Articles Planned for Future Volumes 10
Chapter 1. Rhodopsin: A Prototypical G Protein-Coupled Receptor 12
I. Structure and Function of Rhodopsin: A Prototypical G Protein-Coupled Receptor 13
II. Spectral Tuning and the Mechanism of the Opsin Shift 21
III. Light-Induced Conformational Changes in Rhodopsin 24
IV. Molecular Switches and Determinants of the Active Receptor Conformation 31
V. Coupling of Light-Induced Conformational Changes to Transducin Activation 33
VI. Structural Modeling of Rhodopsin 36
VII. Rhodopsin Mutations as a Cause of Human Disease 39
VIII. Conclusions 40
References 41
Chapter 2. Cell Membrane and Chromosome Replication in Bacillus subtilis 46
I. Introduction 47
II. Early Evidence of Membrane–Chromosome Association 47
III. Chromosome Initiation Mutants of Bacillus subtilis 50
IV. Preparation of Origin–Membrane and Terminus–Membrane Complexes 50
V. The dnaB Gene: Critical for Chromosome Initiation and Replication Origin Membrane Attachment 51
VI. Chromosomal Membrane Attachment Sites 55
VII. In Vitro Initiation of Chromosome Replication Using the Membrane Fraction 57
VIII. Membrane Attachment to the Terminus 58
IX. Differences in Replication Initiation in Two Systems 58
X. Unsolved Questions 58
References 62
Chapter 3. Stability and Structure of Model DNA Triplexes and Quadruplexes and Their Interactions with Small Ligands 66
I. Triple-Helical Structures 68
II. Guanine Quadruplex Structures 90
III. Summary 102
References 102
Chapter 4. On the Physiological Role of Casein Kinase II in Saccharomyces cerevisiae 106
I. General Properties of CKII 107
II. Saccharomyces cereoisiae CKII 111
III. Potential Functions of CKII in Saccharomyces cerevisiae 120
IV. Substrates of CKII in Saccharomyces cerevisiae 130
V. The Physiological Role of CKII 138
References 140
Chapter 5. The Heparan Sulfate„Fibroblast Growth Factor Family: Diversity of Structure and Function 146
I. Diversity and Ubiquity of the Fibroblast Growth Factor Family 147
II. Diversity of Structure and Function 153
III. Structure, Assembly. and Control of the FGF Receptor Complex 166
IV. The FGF Family in Liver Growth and Function 175
V. The FGF Family in Prostate and Prostate Tumors 179
References 184
Chapter 6. The Ribosomal Elongation Cycle and the Movement of tRNAs across the Ribosome 188
I. Introduction 189
II. Functional Aspects: Models of the Elongation Cycle 191
III. Structural Aspects: The Shape of Ribosomes and the Localization of tRNAs 203
IV. Conclusions 216
References 217
Chapter 7. Life on the Salvage Path: The Deoxynucleoside Kinases of Lactobacillus acidophilus R-26 220
I. Historical Background–Nucleotide Metabolism in Lactobacilli 222
II. Purification of' Deoxynucleoside Kinases from Lactobacillus acidophilus R-26 227
III. Steady-state Kinetics 239
IV. Assignment of Subunit Functions 245
V. Cloning the Genes for dAK/dCK or dAK/dGK 247
VI. dCK and dGK are Products of the Same Gene 253
VII. Probing the Active Site and Subunite Contacts 258
VIII. Summary 265
References 267
Chapter 8. Molecular Analyses of Metallothionein Gene Regulation 272
I. Overview of Metallothioneins 273
II. Metallothionein Gene Regulation 274
III. Metallothionein Promotor Organization and Function 276
IV. MRE-Binding trans-Acting Factors 289
V. Conclusions and Suggestions for Further Research 300
References 300
Chapter 9. Transcriptional Regulation of the Steroid Receptor Genes 304
I. Structure of a Steroid Receptor Gene 305
II. Molecular Mechanism of Transcription 306
III. Regulation of the Androgen Receptor Gene 308
IV. Regulation of the Glucocorticoid Receptor Gene 313
V. Regulation of the Progesterone Receptor Gene 315
VI. Regulation of the Estrogen Receptor Gene: Characterization of the 5' Flanking Region 316
VII. Concluding Remarks 318
References 319
Chapter 10. Molecular Evolution of Snake Toxins: Is the Functional Diversity of Snake Toxins Associated with a Mechanism of Accelerated Evolution? 322
I. About Snake Toxins 324
II. Snake Toxins with a Phospholipase A2-Type Fold 326
III. Snake Toxins with a Three-Fingered Fold 354
IV. General Conclusion on the Evolution of Snake Toxins 371
References 372
Index 
380 

Textauszug

Rhodopsin: A Prototypical G Protein-Coupled Receptor

Thomas P. Sakmar    The Howard Hughes Medical Institute, Laboratory of Molecular Biology and Biochemistry, Rockefeller University,New York, New York 10021

Abstract

A variety of spectroscopic and biochemical studies of recombinant site-directed mutants of rhodopsin and related visual pigments have been reported over the past 9 years. These studies have elucidated key structural elements common to visual pigments. In addition, systematic analysis of the chromophore-binding pocket in rhodopsin and cone pigments has led to an improved understanding of the mechanism of the opsin shift, and of particular molecular determinants underlying color vision in humans. Identification of the conformational changes that occur on rhodopsin photoactivation has been of particular recent concern. Assignments of light-dependent molecular alterations to specific regions of the chromophore have also been attempted by studying native opsins regenerated with synthetic retinal analogs. Site-directed mutagenesis of rhodopsin has also provided useful information about the retinal-binding pocket and the molecular mechanism of rhodopsin photoactivation. Individual molecular groups have been identified to undergo structural alterations or environmental changes during photoactivation. Analysis of particular mutant pigments in which specific groups are locked into their respective “off” or “on” states has provided a framework to identify determinants of the active conformation, as well as the minimal number of intramolecular transitions required to switch between inactive and active conformations. A. simple model for the active state of rhodopsin can be compared to structural models of its ground state to localize chromophore-protein interactions that may be important in the photoactivation mechanism. This review focuses on the recent functional characterization of site-directed mutants of bovine rhodopsin and some cone pigments. In addition, an attempt is made to reconcile previous key findings and existing structural models with information gained from the analysis of site-directed mutant pigments. © 1998 Academic Press

I Structure and Function of Rhodopsin: A Prototypical G Protein-Coupled Receptor

Visual pigments comprise a branch of a large family of G protein1-coupled receptors (1). Although they share many similarities with other G protein-coupled receptor types, there is significant specialization in visual pigments not found in other receptor families. In particular, pigments are made up of opsin apoprotein plus chromophore. The chromophore is a cofactor and not a ligand in the classical sense because it is linked covalently via a protonated Schiff base bond to a specific lysine residue in the membrane-embedded domain of the protein (Fig. 1). One of two retinoids serve as the chromophore for nearly all visual pigments. The chromophore in most vertebrate pigments is the aldehyde of vitamin A, 11-cis-retinal (Fig. 2). The chromophore in many invertebrate, fish, and amphibian pigments is the aldehyde of vitamin A2, 11-cis-3-dehydroretinal, which contains an additional carbon-carbon double bond in the β-ionone ring. An important structural feature of the retinal chromophore in rhodopsin, in addition to its Schiff base linkage, is its extended polyene structure, which accounts for its visible absorption properties and allows for resonance structures (2).

Fig. 1 Schematic representation of bovine rhodopsin secondary structure based on previous models. Seven putative TM helices, which are characteristic of G protein-coupled receptors, are shown. The carboxyl terminus and cytoplasmic surface are toward the top, and the amino terminus and extracellular (intradiskal) surface are toward the bottom of the figure. Rhodopsin resides in the specialized disk membrane of the outer segment of the rod cell of the retina and is responsible for dim-light (scotopic) vision. Lys296 is the site of the retinylidene Schiff base linkage. Glu113 is the negatively charged counterion to the positively charged protonated Schiff base. An essential disulfide bond on the intradiskal surface links Cys110 and Cys187. Cys322 and Cys323 in the carboxyl-terminal tail are palmitoylated, which results in a fourth cytoplasm loop.

Fig. 2 (A) Photoisomerization of the 11-cis-retinylidene chromophore to the all-trans form is the only light-dependent event in vision. The 11-cis-retinal chromophore is covalently linked as a cofactor to Lys296 on TM helix 7 via a protonated Schiff base bond. Important photochemical properties of rhodopsin in the disk membrane include a very high quantum efficiency (~0.67 versus < 0.2 for 11-cis-retinal in solution) and an extremely low rate of thermal isomerization of the chromophore (~2.25 × 1010 slower than in solution). (B) The UV–visible absorption spectrum of purified recombinant COS cell rhodopsin in detergent solution shows a characteristic broad visible absorbance with a λmax value of 500 nm. The 280-nm peak represents the protein component. After exposure to light, the pigment is converted to a species with a λmax, value of 380 nm, characteristic of metarhodopsin II. This is the active form of the receptor that interacts with the G protein, transducin. Identical results can be obtained with rhodopsin from bovine retinas purified by concanavalin-A lectin affinity chromatography.

Rhodopsin has a broad visible absorption maximum (λmax) at about 500 nm. On photoisomerization of the chromophore, the pigment is converted to metarhodopsin II (MII) with a λmax value of 380 nm (Fig. 2). The MII intermediate is characterized by a deprotonated Schiff base chromophore linkage. MU is the active form of the receptor (R*, light-activated rhodopsin), which catalyzes guanine nucleotide exchange by transducin.

Photoisomerization of the 11-cis to all-trans form of the retinylidene chromophore is the primary event in visual signal transduction, and it is the only light-dependent step (Fig. 2). Chromophore isomerization activates the pigment, allowing it to interact with a specific heterotrimeric G protein, trans-ducin. In the case of the vertebrate visual system, transducin activation leads to the activation of a cyclic-GMP phosphodiesterase, and the closing of cyclic-GMP-gated cation channels in the plasma membrane of the rod cell. Light causes a graded hypeipolarization of the photoreceptor cell. The amplification, modulation, and regulation of the light response is of great physiological importance and has been discussed in detail elsewhere (3–5). However, it should be pointed out that despite the fact that the visual system functions over about a 106-fold range of light intensity, the retinal rod cell has single-photon detection capability due to extremely low levels of dark noise in rhodopsin and a significant degree of biochemical amplification. Thermal isomerization in a single rhodopsin molecule at physiologic temperature has been estimated to occur about once in 470 years (6). Activation of a single rhodopsin molecule by a single photon can prevent the entry of as many as 108 cations into the rod cell. The possibility of single-pheromone molecule detection by insect olfactory systems notwithstanding, the visual system is unique among sensory signal transduction systems in that it can detect single events.

The visual pigments of many species of vertebrates and invertebrates have been studied by absorption spectroscopy or microspectrophotometry of visual organs. Therefore, historically vertebrate visual pigments have been generally classified based on the photoreceptor cell type of the retina in which they are found (7). Rod cells, responsible for dim-light vision, contain rhodopsin (“red” opsin). Cone cells, responsible for bright-light and color vision, contain iodopsins (“violet” opsins), also known as cone pigments or color vision pigments. The cloning of opsins from a variety of species has allowed more detailed comparisons and phylogenetic classifications based on structural, spectral, and biochemical properties of visual pigments (8). The homology in the opsin family of genes indicates that divergent evolution occurred from a single precursor retinal-binding protein to form long- and short-wavelength-absorbing prototypes. The long-wavelength prototype diverged to form red and green pigments. The short-wavelength prototype then diverged to form a blue pigment and the family of rhodopsins and rhodopsin-like green pigments.

Each visual pigment is tuned to a particular wavelength of maximal absorption, λmax, although the visible absorbance peak tends to be quite broad. Even though a protonated retinylidene Schiff base chromophore is likely to be universal in visual pigments, the λmax values of visual pigments span the visible spectrum (i.e., from near-ultraviolet at about 400 nm to far visible red at about 600 nm). Distinct chromophore–protein interactions are responsible, directly or indirectly, for spectral tuning in visual pigments. Thus, differences in primary structure result in differences in spectral properties.

Bovine rhodopsin is the most extensively studied G protein-coupled receptor. A large amount of pigment (0.5–1.0 mg) can be obtained from a single bovine retina by sucrose density gradient...

Produkt-Details

• Erscheint lt. Verlag: 9.2.1998
• Sprache: englisch
• Themenwelt: Sachbuch/Ratgeber ► Natur / Technik ► Natur / Ökologie
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Angewandte Physik
• Themenwelt: Technik
• ISBN-10: 0-08-086347-7 / 0080863477
• ISBN-13: 978-0-08-086347-4 / 9780080863474