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Showing papers in "Annual Review of Biochemistry in 1984"


Journal ArticleDOI
TL;DR: The current models for the complexes of Cro, repressor, and CAP with operator DNA are probably fundamentally correct, but it should be emphasized that model building alone, even when coupled with genetic and biochemical studies, cannot be expected to provide a completely reliable "high-resolution" view of the protein-DNA complex.
Abstract: Several general principles emerge from the studies of Cro, lambda repressor, and CAP. The DNA-binding sites are recognized in a form similar to B-DNA. They do not form cruciforms or other novel DNA structures. There seem to be proteins that bind left-handed Z-DNA (87) and DNA in other conformations, but it remains to be seen how these structures are recognized or how proteins recognize specific sequences in single-stranded DNA. Cro, repressor, and CAP use symmetrically related subunits to interact with two-fold related sites in the operator sequences. Many other DNA-binding proteins are dimers or tetramers and their operator sequences have approximate two-fold symmetry. It seems likely that these proteins will, like Cro, repressor, and CAP, form symmetric complexes. However, there is no requirement for symmetry in protein-DNA interactions. Some sequence-specific DNA-binding proteins, like RNA polymerase, do not have symmetrically related subunits and do not bind to symmetric recognition sequences. Cro, repressor, and CAP use alpha-helices for many of the contacts between side chains and bases in the major groove. An adjacent alpha-helical region contacts the DNA backbone and may help to orient the "recognition" helices. This use of alpha-helical regions for DNA binding appears to be a common mode of recognition. Most of the contacts made by Cro, repressor, and CAP occur on one side of the double helix. However, lambda repressor contacts both sides of the double helix by using a flexible region of protein to wrap around the DNA. Recognition of specific base sequences involves hydrogen bonds and van der Waals interactions between side chains and the edges of base pairs. These specific interactions, together with backbone interactions and electrostatic interactions, stabilize the protein-DNA complexes. The current models for the complexes of Cro, repressor, and CAP with operator DNA are probably fundamentally correct, but it should be emphasized that model building alone, even when coupled with genetic and biochemical studies, cannot be expected to provide a completely reliable "high-resolution" view of the protein-DNA complex. For example, the use of standard B-DNA geometry for the operator is clearly an approximation.(ABSTRACT TRUNCATED AT 400 WORDS)

1,480 citations


Journal ArticleDOI
TL;DR: Allysine and Hydroxyallysine Pathways Pathways, Allysine-Hydroxypyridinium Residues, and Methods for Analysis: Alternative M echanisms and Methods are presented.
Abstract: PERSPECTIVES AND SUMMARy 717 LYSYL OXIDASE 719 COLLAGEN 720 Allysine and Hydroxyallysine Pathways 720 Hydroxypyridinium Residues... ... 724 Molecular Sites 730 Basement Membranes 733 Methods oj Analysis 734 Alternative M echanisms ..... ... 734

1,121 citations


Journal ArticleDOI
TL;DR: All glycosyl residues (except the residue at the reducing end of an oligosaccharide, which is called a glycose residue) are glycosidically linked at C-l and this fact is assumed in the notation used, and, thus, C-\ is not mentioned.
Abstract: 1 Abbreviations and conventions used: AceA, aceric acid (3-C-carboxy-5-deoxy-L-xylose); Api, apiose; Ara, arabinose; Fuc, fucose; Gal, galactose; GalVA, galacturonic acid; Glc, glucose; GlcA, glucuronic acid; Rha, rhamnose; Xyl, xylose; PGA lyase, endo-IX-I,4polygalacturonic acid lyase; and PIIF, Proteinase Inhibitor Inducing Factor. All glycosyl residues are in the pyranoid ring form unless the furanoid form is indicated, e.g. Ara! Standard D and L notations are used when the absolute configuration of a particular glycosyl residue has been experimentally determined. When the absolute configuration has not been experiment­ ally determined, we omit the D or L notation, although in all cases studied the glycosyl residues Gal, Glc, Xyl, GalA, and GlcA have been found in the D configuration, and the glycosyl residues Fuc, Ara, and Rha in the L configuration. We use in this review a simplified linkage notation. All glycosyl residues (except the residue at the reducing end of an oligosaccharide, which is called a glycose residue) are glycosidically linked at C-l. This fact is assumed in the notation used, and, thus, C-\ is not mentioned. For example, a glycosyl residue designated as "terminal" (T) is glycosidically linked to another glycosyl or glycose residue only through C-J and contains no glycosyl residues linked to it. A glycosyl residue designated as 2-linked is glycosidicaUy linked to another glycosyl or glycose residue through C-J and has another glycosyl residue linked to it at 0-2. A glycosyl residue designated as 3,6-linked is glycosidically linked to another sugar through C-l and has glycosyl residues linked to it at 0-3 and 0-6; therefore, such a residue represents a branch point in a complex carbohydrate. The linkage from C l is also assumed in the notation for oligosac­ charides. Thus, L-Fuc � 2-D-Gal is a disaccharide in which an L-fucosyl residue is attached by an ()(-glycosidic bond from its C-l to 0-2 of a D-galactose residue. 2 Present address: Department of Bot

991 citations


Journal ArticleDOI
TL;DR: Z-DNA in Other Naturally Occurring Sequences, e.g. d(CA/GT}n, Drosophilia and Chironomus, and Other Species : 831.
Abstract: CONTENTS PERSPECTIVE AND SUMMARY 792 INTRODUCTION 793 MOLECULAR STRUCTURE OF Z-DNA 795 METHODS FOR DETECTING Z-ONA 803 Physical-Chemical Methods 804 Use of Specific Anti-Z-DN A Antibodies 806 PHYSICAL-CHEMICAL STUDIES OF Z-DNA 809 Ultraviolet Circular Dichroism and Absorbance 809 Raman Spectra 810 Nuclear Magnetic Resonance Studies 8 1 1 Other Methods 813 Theoretical Analyses: Energetics and Mechanics 813 CHEMICAL FACTORS INFLUENCING THE EQUILIBRIUM BETWEEN BAND Z-DNA 816 Covalent DN A Modifications 816 Ions, Solvents, and Small Molecules 818 Cytosine Methylation in CG Sequences Stabilizes Z-DNA 819 NEGATIVE SUPERCOILING STABILIZES Z-DNA 821 Topological Constraints in DN A 821 Form V DNA 825 PROTEINS THAT BIND TO Z-DNA 826 NUCLEOTIDE SEQUENCES THAT FAVOR Z-DNA FORMATION 828 Polymers and Repetitive Sequences, e.g. d(CA/GT}n 828 Z-DNA in Other Naturally Occurring Sequences 829 CYTOLOGICAL STUDIES OF Z -DNA IN CHROMOSOMES 830 Drosophilia and Chironomus 830 Other Species : 831

977 citations



Journal ArticleDOI
TL;DR: This chapter discusses the regulation of Ribosomal Protein Genes and their Transcription in the context of ribosomal RNA regulation.
Abstract: CONTENTS PERSPECTIVES AND SUMMARY 75 REGULATION OF RIBOSOMAL PROTEIN SyNTHESIS 77 Organization of Ribosomal Protein Genes ...... 78 Translational Feedback Regulation 78 Transcription of Ribosomal Protein Genes and I ts Regulation 91 REGULATION OF rRNA AND RIBOSOME SyNTHESIS 9S Organization ofrRNA Genes and Their Transcription 96' Stringent Control 99 Growth Rate-Dependent Control 101 O ther Possible Modes of R egulation 109

803 citations


Journal ArticleDOI
TL;DR: The primary structure of rRNA Species-Nomenclature and the secondary structure of Secondary-Structure are investigated in more detail in this chapter.
Abstract: PERSPECTIVES AND SUMMARy............................................................................................................. 119 rRNA Species-Nomenclature .. ... ... ... ... .... .. ............................ ... ... ..... .. ... .... ... .. ... .... .... . 120 PRIMARY STRUCTURE............................................................................................................................ 121 SECONDARY STRUCTURE....................................................................................................................... 124 General Approaches ....................... ... .. .. ... .. ... .. . . . .. ........................ .... ... .. .... .. .... ... . .. ... .. 124 Description of Secondary-Structure M ode/s......... ... ....... ... ........... ... .. . ....... ..................... .. 129 Phylogenetic Comparison ............ . .. . .... ... .. ... .. . .... ... .. .................... ... ... ... ... .. . ... .... ..... .. .. 136 Experimental Tests.... . . .. .. ....... ........ ... .... .. . .. ... ................ ... .. ... ........ .... .. .... ............... .. . ... 136

765 citations


Journal ArticleDOI
TL;DR: At Atomic-level details are now in hand for many of the interactions that hold fibrin units together, although some aspects have yet to be resolved.
Abstract: Fibrinogen is a soluble plasma protein that is converted to polymeric fibrin in response to damage to the vascular system The clotting process is initiated when platelets aggregate at the wound site Their disruption releases biologically active amines and a proteolytic cascade follows which culminates in the conversion of fibrinogen to fibrin The fibrin polymer forms the matrix of the tangle of cellular and molecular substances called the blood clot Atomic-level details are now in hand for many of the interactions that hold fibrin units together, although some aspects have yet to be resolved Of necessity, fibrin clots need to be dismantled when they are no longer needed, an operation largely accomplished by the proteolytic enzyme plasmin Various regulatory phenomena are involved in maintaining the balance between intravascular fluidity and clots that prevent blood loss A variety of hereditary conditions, including mutant fibrinogens, can predispose individuals to either thrombosis or bleeding Key concepts: The underlying fabric of blood clots is a protein polymer called fibrin Fibrin clots are formed in response to injuries to any part of the vascular system The conversion of soluble fibrinogen molecules to insoluble fibrin depends on thrombin generated from prothrombin Keywords: fibrinogen; fibrin; clot stabilisation; fibrinolysis; blood clotting; X-ray structures

716 citations




Journal ArticleDOI
TL;DR: Protein Subunits Buried Between Protein Subunits and Secondary-Structure Surfaces and Residue Composition 564 Chemical Character of Buried and Accessible Surfaces 564 Extent of the Accessible and Buried Sur surfaces 565 Surfaces Buried between protein Subunits 566.
Abstract: PERSPECTIVES AND SUMMARy 538 CONFORMATION OF HELICES, PLEATED SHEETS, AND SIDE CHAINS 539 Hydrogen Bonds 539 IX Helices : 539 Left-Handed IX Helices, Polyproline Helices, and Turns 540 P Sheets: Twisting and Coiling 540 P Sheets: P Bends and P Bulges 541 Side Chains 542 CLOSE PACKING IN PROTEINS 544 Protein I nteriors 544 Protei?"! Surfaces 546 PACKING OF IX HELICES AND P SHEETS 546' Packing of Ct Helices 547 IX-Helix-p-Sheet Packing 549 Packing of P Sheets 552 Residue Composition and Packing in p Sheets 556 CHAIN TOPOWGY IN PROTEINS 557 CLASSIFICATION OF PROTEIN STRUCTURES 559 PROTEIN STABILITY: HYDROGEN BONDS, HYDROPHOBICITY, AND SURFACE AREAS 560 Hydrogen Bonds 560 Hydrophobicity and Surface Areas 561 Residue Surfaces and Environments 562 Secondary-Structure Surfaces and Residue Composition 564 Chemical Character of Buried and Accessible Surfaces 564 Extent of the Accessible and Buried Surfaces 565 Surfaces Buried Between Protein Subunits 566

Journal ArticleDOI
TL;DR: This work has shown clear trends in the development of closed-to-Open Promoter Transition and Analysis of the Open mode, and these trends are likely to continue into the next generation of drugs.
Abstract: CONTENTS Perspectives and Summary .. Components of the System .. Location of the Promoter by RNA Polymerase .. The Closed Promoter-Polymerase Interaction .. The Closed-to-Open Promoter Transition and Analysis of the Open

Journal ArticleDOI
TL;DR: The present review focuses on the structure of the polyprotein Gene Structures of the Precursor Polypeptide and the approaches used in terms of Peptide approach, strategy, and values.
Abstract: PERSPECTIVES AND SUMMARy 666 SCOPE OF THE REVIEW 668 CHARACTERISTICS OF THE PRECURSORS 669 Sites of Synthesis of Precursors 672 APPROACHES AND STRATEGIES USED IN CHARACTERIZING THE PRECURSOR PROTEINS....... 673 The Peptide Approach 674 The Nucleic Acid Approach 675 STRUCTURE OF POLYPROTEIN GENES 679 Isolation of Genomic Clones 679 Polyprotein Genes in Which Exons Do Not Represent Individual Functional Domains of the Precursor M olecule 680 Polyprotein Genes in Which Exonic Regions Represent Individual Bioactive Domains of the Precursor Polypeptide 682 Nonmammalian Polyprotein Gene Structures 684

Journal ArticleDOI
TL;DR: The present work presents a meta-analysis of RNA regulation through the lens of chunk structure replacement, which shows clear trends in both the maintenance and replacement of single-stranded RNAs.
Abstract: PERSPECTIVES AND SUMMARY 573 GENOMIC ORGANIZATION 574 TRANSCRIPTIONAL MAPPING 576 INITIATION, ELONGATION, AND TERMINATION OF TRANSCRIPTION 578 I n Vivo Transcription 578 In Vitro Transcription 581 PROCESSING OF PRIMARY TRANSCRIPTS 582 POST-TRANSCRIPTIONAL MODIFICATION AND MATURATION OF RNA ..•..• ••...• 584 Ribosomal RN As 584 Transfer RNAs 586 Messenger RNAs 587 "7S RNA" 588 OVERALL MODE OF TRANSCRIPTION 590 CONCLUSIONS AND PROSPECTS 592

Journal ArticleDOI
TL;DR: A comparison of the Oligonucleotide Probe and Primer Approaches for Synthetic DNA-Mediated Mutagenesis on Single-Stranded Bacteriophage DNA vs Plasmid DNA Templates and other approaches.
Abstract: PERSPECTIVES AND SUMMARy 323 CHEMICAL SYNTHESIS AND CLONING OF OLlGODEOXYRIBONUCLEOTIDES 324 Solid-Phase Synthesis of Oligonucleotides 325 Assembly of Oligonucleotides on a Solid Support 325 Deblocking of Fully Protected Oligonucleotides 328 Purification of Polynucleotides 330 Characterization of Oligonucleotides 332 Comparison of Phosphotriester and Phosphite-Triester Methods 332 Cloning of Synthetic DN A 333 Use of Synthetic Genes 335 THE ROLE OF SYNTHETIC DNA IN THE ISOLATION OF GENES 336 Oligonucleotides as Hybridization Probes 337 Oligonucleotides as Specific Primers 340 Comparison of the Oligonucleotide Probe and Primer Approaches 342 SYNTHETIC DNA-MEDIATED SITE-SPECIFIC MUTAGENESIS 343 Synthetic Oligonucleotide-Mediated Mutagenesis on Single-Stranded Bacteriophage DNA vs Plasmid DNA Templates 344 Selection and Detection of Synthetic Oligonucleotide-Generated Mutants 347 Increasing the E,fjiciencies �r Synthetic DNA-Mediated Mutagenesis 348 Other Approaches to Oligonucleotide-Directed Mutagenesis 350



Journal ArticleDOI
TL;DR: The biochemical process described by nitrogen fixation is the reduction of N2 to NH3, which can then be used for the synthesis of amino acids, nucleic acids, and other essential nitrogenous compounds, which ranks with photosynthesis as a process of fundamental importance to all life on earth.
Abstract: Publisher Summary Nitrogen fixation ranks with photosynthesis as a process of fundamental importance to all life on earth. The biochemical process described by nitrogen fixation is the reduction of N2 to NH3, which can then be used for the synthesis of amino acids, nucleic acids, and other essential nitrogenous compounds. Intensive agricultural methods have led to increased use of and dependence on manufactured nitrogenous fertilizers with decreased emphasis on biological nitrogen fixation. However, with the depletion of fossil fuels, the cost of fertilizer production is rising, and this situation could easily lead to a worldwide food crisis. One aspect of nitrogen fixation that is receiving an increased amount of interest is the role of the element molybdenum. The enzyme nitrogenase that catalyzes the reduction of N2 to NH3 is one of a handful of enzymes that relies absolutely on Mo for catalytic activity. This fact has practical significance for agriculture since certain soils that could just barely support the growth of nitrogen-fixing legumes and could be greatly improved simply by addition of trace levels of Mo.


Journal ArticleDOI
TL;DR: The artist, who lived through the two world wars and was lucky to leave Germany in 1931 to live in Denmark, got the opportunity to come and settle in the United States when he was already 40 years old.
Abstract: I was born in the middle of the last year of the last century, in the city of Konigsberg, the capital of East Prussia. It is now Russian and its name is Kaliningrad. I lived through the two world wars and was lucky to leave Germany in 1931 to live in Denmark, where I worked for seven years. In 1939, shortly before the outbreak of the second world war, I got the opportunity to come and settle in the United States when I was already 40 years old. My work was not unknown, but also not well known.