Design of DNA-binding peptides based on the leucine-zipper motif

Article Abstract:

The genetic material of a cell is not, of course, floating loose within a cell; it must be combined with a myriad of proteins which provide critical structural and regulatory functions. The regulatory proteins must be able to interact with specific genes by turning them on or off, as the cell requires. To learn what aspects of regulatory proteins are critical to their normal function, researchers have applied a 'minimalist' approach to the study of the leucine zipper proteins. The minimalist approach involves the design and synthesis of novel proteins, ones which have retained only certain specific features of a natural protein. If the new protein retains the function of the original protein, the retained features contain the amino acids critical to the protein's function, while the changed amino acids obviously do not. Leucine zipper proteins get their name from the presence of a leucine amino acid residue every seventh position down the protein chain. These leucines are responsible for two protein chains being held together in parallel, hence the 'zipper' analogy. At the amino end of the protein, however, is a group of basic amino acids, which are responsible for recognizing a specific sequence on the DNA chain. Researchers synthesized a 'minimal' protein containing only the basic amino acids and leucines hypothesized to be critical, and produced a novel molecule retaining the same DNA-binding characteristics. The basic region appears to form a helix, which lies in the major groove of the coiled DNA molecule in regions where the sequence of four DNA bases is just right. The amino acids facing the solvent side of the protein do not get involved in this specific interaction, and can be changed without altering the DNA-binding properties of the molecule. This research not only provides insight into the structures important for regulatory proteins, but also demonstrates the power of the minimalist approach to analyzing the functions of proteins. (Consumer Summary produced by Reliance Medical Information, Inc.)

Nucleotide sequence, Base sequence, DNA binding proteins

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Proteins from scratch

Article Abstract:

Researchers have developed a single computational algorithm that simplifies de novo protein design. The algorithm predicts an optimal protein sequence for a given fold to produce a desired three-dimensional structure.

Models, Proteins, Protein synthesis, Protein folding, Protein engineering

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Splice-site selection and decoding: are they related?

Article Abstract:

Aminoglycoside antibiotics bind to RNA elements in both 16S RNA and in group I introns. A model showing common functional and structural elements in both decoding and splicing is presented.

Antibiotics, RNA splicing, Introns

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