Protein-nucleic acid complexes

A number of studies report novel DNA binding interfaces. Wojciak et al. 

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PDB Research Col-laboratory for Structural Bioinformat-ics (RCSB) macromole-cular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses nu- meric. biblio. -20000 records experi- ments Research Col-laboratory for Structural Bioinformatics online, CD-ROM periodi- cally WU7W.TCsh.0Tg/ pdh/... 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

Standard calculation methods developed for small proteins are sufficiently powerful to solve protein structures and complexes in the 30 kDa range and beyond [97,98] and protein-nucleic acid complexes [99]. Torsion angle dynamics offers increased conver-... 

NUCLEOPROTEINS. Nucleoprotein conjugates have many roles in the storage and transmission of genetic information. Ribosomes are the sites of protein synthesis. Virus particles and even chromosomes are protein-nucleic acid complexes. 

Uranyl acetate b 1-2%, pH 4.2-4.5 Protein—nucleic acid complexes Ribosomes Tubulin Sogo et al. (45) Khulbrandt and Unwin (47) MandelkowandMandelkow (46)... 

Tab. 9.3 Observed trans hydrogen bond couplings in protein-nucleic acid complexes ...

Protein-Nucleic Acid Complexes 9.2.3.1 h2JNN-Couplings... 

Experimental method Protein Nucleic acids Protein-nucleic acid complexes Others Total... 

There have been two basic approaches. First one involves isolation of the chromatin and nucleosome from the healthy and diseased cell line. The second approach is the reconstitution of the model target such as nucleosome followed by the association with the drug(s). The second approach has been extensively employed to identify the binding site in the protein-nucleic acid complex. A pre-knowledge about the components and their arrangements in the reconstituted system sometime makes it the preferred approach. Different biophysical, biochemical and genetic techniques have been employed to understand the mode of association and the effect of the drugs upon chromatin/nucleosome structure and function. 

Negative entropy is also expressed in the ordered three-dimensional structures of complex proteins, protein-nucleic acid complexes, molecular machines, biological membranes, and so on. Metabolism and chemical signaling too are highly and meticulously ordered processes. Use your brain to think about the brain the degree of order in the creation of trillions of connections among nerve cells that is required to allow us have that most amazing facility, consciousness. 

An imderstanding of the mechanism by which the highly specific and selective recognition of a nucleotide sequence is achieved is only possible with knowledge of the structural details of specific protein-nucleic acid complexes. For the regulation of gene activity the binding of proteins to double-stranded DNA is of central importance. We... 

The Nature of the specific Interactions in Protein-Nucleic Acid Complexes... 

Splicing occurs in a large protein-nucleic acid complex, termed the spUceosome. Components of the spliceosome are, apart from the pre-mRNA, a number of proteins and small RNAs, termed the Ul, U2, U4, U5 and U6. The RNAs found in the spUceo-some are bound to specific proteins. The complexes are termed snRNPs (small nuclear ribonucleoprotein). Depending upon the type of RNA bound, there are Ul, U2, U5 and U4/U6 snRNPs. 

E. Palecek, and co-workers, in D. M. J. Lilley, H. Heumann, and D. Suck, eds., Structural Toolsfor the Analysis of Protein-Nucleic Acid Complexes, Birkhauser, Basel, Switzerland, 1992, pp. 1—22. 

PDB is one of the oldest protein data bases, founded in 1971. It has three locations, Rutgers University in New Jersey, San Diego Supercomputer Center (SDSC) at the University of California, and the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. The PDB is a source for protein characterization and structure as well. The PDB archive contains macromolecular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses. Approximately 50-100 new structures are deposited each week, which are annotated and released upon the depositor s specifications. PDB data are freely available worldwide. PDB formats, annotates, validates, and releases dozens of complicated structure files each week some of them take only a couple of hours, others take weeks to process. Data processing is the main task of people at the PDB and validation is the most time-consuming part (Smith-Schmidt, 2002). 

Protein-Nucleic Acid Complexes. During protein purification it occasionally becomes necessary to remove basic proteins or contaminating nucleic acids. The controlled addition of sparingly soluble... 

The work of many laboratories has provided significant insight into the detailed workings of Pol III function at the replication fork. The way in which the replisome interacts with other DNA processes (i.e., DNA compaction, transcription, and recombination, repair), however, is poorly understood. For example, how does Pol III holoenzyme replicate through high-affinity protein-nucleic acid complexes such as RNA polymerase or repressor proteins What is the fate of the replication components after an encounter with a blocking lesion Does the replisome... 

Kantardjieff KA, Rupp B. Matthews coefficient probabilities improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci. 2003 12 1865-1871. 

Nucleic acids, protein-nucleic acid complexes and related... 

An interesting metal-binding motif in proteins is the zinc finger, which contains a / ribbon-turn-a helix motif that binds a zinc ion via four sulfur atoms of cysteine residues, or via two such sulfur atoms and two nitrogen atoms (from histidine). This motif, first identified by NMR studies, has been found in the crystal structures of several protein-nucleic acid complexes. ... 

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