Protein-nucleic acid assemblies

The observation that nucleocapsid assembly in the absence of nucleic acids was inhibited indicated that interaction of the coat protein with the RNA is an essential and early step in the assembly pathway. The availability of mutant coat proteins that retained nucleic acid-binding activity but could not assemble further provided an opportunity to identify a possible coat protein-nucleic acid assembly intermediate. Cross-linking experiments revealed the presence of a coat protein dimer that could be detected only in the presence of nucleic acid and for those types of mutant proteins that had retained nucleic acid-binding activity. The protein dimer itself could not assemble into cores but was incorporated into cores in the presence of wild-type protein. These and other results strongly suggested that the cross-linked dimer represents a genuine intermediate of nucleocapsid core assembly. 

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read several different structural file formats and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. 

There are three chemical problems associated with the assembly of a protein, nucleic acid, or other biopolymer. The first is to overcome thermodynamic barriers. The second is to control the rate of synthesis, and the third is to establish the pattern or sequence in which the monomer units are linked together. Let us look briefly at how these three problems are dealt with by living cells. 

A schematic block diagram of the metabolism of a typical aerobic heterotroph. The block labeled Catabolism represents pathways by which nutrients are converted to small-molecule starting materials for biosynthetic processes. Catabolism also supplies the energy (ATP) and reducing power (NADPH) needed for activities that occur in the second block these compounds shuttle between the two boxes. The block labeled Biosynthesis represents the synthesis of low- to medium-molecular-weight components of the cell as well as the synthesis of proteins, nucleic acids, lipids, and carbohydrates and the assembly of membranes, organelles, and the other structures of the cell. 

The chemical polymerization of even a moderately sized protein of a hundred amino acids in the laboratory is extremely laborious, and the yields of active product can often be low to zero (Kent and Parker, 1988). Cells accomplish this task by using an intricate mechanism which involves catalytic machinery composed of proteins, nucleic acids and their complexes, and synthesize polypeptide chains that are composed of hundreds of amino acids. This process is depicted in Fig. 2.4, and is described in the sections below. The basic components of the cellular protein synthesis apparatus, in all known biological systems, are ribosomes, which are aggregate structures containing over fifty distinct proteins, and three distinct molecules of nucleic acid known as ribosomal ribonucleic acid (ribosomal RNA or rRNA). The amino acids are brought to the ribosomes, the assembly bench , by an RNA molecule known appropriately as transfer RNA . Each of the twenty amino acids is specifically coupled to a set of transfer RNAs (discussed below) which catalyze their incorporation into appropriate locations in the linear sequence of polypeptide chains. Several other intracellular proteins known as init iation and elongation factors a re also required for protein synthesis. 

Heterologous expression systems have been of critical importance for the study of viral assembly at the molecular and structural levels. These systems afford enormous flexibility in terms of dissecting the assembly pathway and investigating protein—protein or protein—nucleic acid interactions in the absence of viral transcription and replication. In addition, moderate- to high-resolution structural analyses of assembly precursors, intermediates, and end products, all generated by expression in heterologous systems, have yielded unprecedented molecular details of the structure and function of virus particles. There can be no doubt that the application of heterologous expression systems will continue to provide answers to unresolved questions about viral assembly and structure. 

Thomas, G. J. Jr. (1999). Raman spectroscopy of protein and nucleic acid assemblies. Annu. Rev. Biophys. Biomol. Struct. 28, 1-27. 

The term macromolecule refers to a variety of compounds, including biologically important compounds such as proteins, nucleic acids, and also many important manmade polymers. They may further aggregate into what are called macromolecular assemblies. The molecular shapes of these compounds, because of their large size, have greater variability and are somewhat different from those of smaller compounds. Their possible conformations are an important component of their biological and chemical function. 

When we solve the structure of a molecule, any kind of molecule, including proteins, nucleic acids, or even large assemblies such as viruses or ribosomes, in the end we seek to identify and specify the Xj, yj, Zj coordinates of every atom in the molecule. The form, the shape, the image, must always first be defined in these simple numerical terms, as ordered triplets. Only from these can we faithfully reproduce the precise structure of the molecule in more familiar visual terms, as pictures or images. 

Synthesis, by contrast, is a complex and meticulous job, like the assembly-line of a car factory, turning out precision-built, highly accurately finished models with the minimum of flaws. Biosynthetic pathways demand that we start with the most primitive of the cell s building blocks - simple acids, carbon dioxide, and a nitrogen-source - and from them build a galaxy of macromolecules, carbohydrates, lipids, proteins, nucleic acids. 

Biomembranes are large flexible sheets that serve as the boundaries of cells and their intracellular organelles and form the outer surfaces of some viruses. Membranes literally define what is a cell (the outer membrane and the contents within the membrane) and what is not (the extracellular space outside the membrane). Unlike the proteins, nucleic acids, and polysaccharides, membranes are assembled by the noncovalent association of their component building blocks. 

Assembly of the large, multiprotein cleavage/polyadenyl-ation complex around the AU-rIch poly(A) signal In a pre-mRNA is analogous In many ways to formation of the transcriptlon-prelnitlatlon complex at the AT-rIch TATA box of a template DNA molecule (see Figure 11-27). In both cases, multiprotein complexes assemble cooperatively through a network of specific protein-nucleic acid and protein-protein Interactions. 

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