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Rop Protein
Rop (also known as repressor of primer, or as RNA one modulator (ROM)) is a small dimeric protein responsible for keeping the copy number of ColE1 family and related bacterial plasmids low in ''E. coli'' by increasing the speed of pairing between the preprimer RNA, RNA II, and its antisense RNA, RNA I. Structurally, Rop is a homodimeric four-helix bundle protein formed by the antiparallel interaction of two helix-turn-helix monomers. The Rop protein's structure has been solved to high resolution. Due to its small size and known structure, Rop has been used in protein design work to rearrange its helical topology and reengineer its loop regions. In general, the Helix_bundle#Four-helix_bundles, four-helix bundle has been extensively used in de novo protein design work as a simple model to understand the relationship between amino acid sequence and structure. External links Rop proteinfrom Proteopedia References {{protein-stub Proteins ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ColE1
ColE1 is a plasmid found in bacteria. Its name derives from the fact that it carries a gene for colicin E1 (the ''cea'' gene). It also codes for immunity from this product with the ''imm'' gene. In addition, the plasmid has a series of mobility (''mob'') genes. Its size and the presence of a single EcoRI recognition site caused it to be considered as a vector candidate. Replication ColE1 replication begins at the origin. 555 bp upstream from this point, RNA polymerase initiates transcription of RNAII which acts as a pre-primer and begins the synthesis of the leader strand. The transcript folds into a secondary structure which stabilises the interaction between the nascent RNA and the origin's DNA. This hybrid is attacked by RNase H, which cleaves the RNA strand, exposing a 3' hydroxyl group. This allows the extension of the leading strand by DNA polymerase I. Lagging strand synthesis is later initiated by a primase encoded by the host cell. Replication is carried out ent ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Plasmids
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria and archaea; however plasmids are sometimes present in and eukaryotic organisms as well. Plasmids often carry useful genes, such as those involved in antibiotic resistance, virulence, secondary metabolism and bioremediation. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain additional genes for special circumstances. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation. Synthetic plasmids are available for procurement over the internet by various vendors ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Antisense RNA
Antisense RNA (asRNA), also referred to as antisense transcript, natural antisense transcript (NAT) or antisense oligonucleotide, is a single stranded RNA that is complementary to a protein coding messenger RNA (mRNA) with which it hybridizes, and thereby blocks its Translation (biology), translation into protein. The asRNAs (which occur naturally) have been found in both prokaryotes and eukaryotes, and can be classified into short (200 nucleotides) non-coding RNAs (ncRNAs). The primary function of asRNA is regulating gene expression. asRNAs may also be produced synthetically and have found wide spread use as research tools for gene knockdown. They may also have therapeutic applications. Discovery and history in drug development Some of the earliest asRNAs were discovered while investigating functional proteins. An example was MicF RNA, micF asRNA. While characterizing the outer membrane Porin (protein), porin in Escherichia coli, ''E.coli'', some of the promoter clones observ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Four-helix Bundle
A helix bundle is a small protein fold composed of several alpha helices that are usually nearly parallel or antiparallel to each other. Three-helix bundles Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains. The three-helix bundle in the villin headpiece domain is only 36 amino acids long and is a common subject of study in molecular dynamics simulations because its microsecond-scale folding time is within the timescales accessible to simulation. The 40-residue HIV accessory protein has a very similar fold and has also been the subject of extensive study. There is no general sequence motif associated with three-helix bundles, so they cannot necessarily be predicted from sequence alone. Three-helix bundles often occur in actin-binding proteins and in DNA-binding proteins. Four-helix bundles Four-helix bundles typically consist of four helices packed in a coiled-coil arrangement with a sterically close-packed hydrophobic core in t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Helix-turn-helix
Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two alpha helix, α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif. Discovery The discovery of the helix-turn-helix motif was based on similarities between several genes encoding Transcription (genetics), transcription regulatory proteins from bacteriophage lambda and ''Escherichia coli'': Cro, Catabolite activator protein, CAP, and cI protein, λ repressor, which were found to share a common 20–25 amino acid sequence that facilitates DNA recognition. Function The helix-turn-helix motif is a DNA-binding motif. The recognition and binding to DNA by helix-turn-helix proteins is done by the two α helices, one occupying the N-terminus, N-terminal end of the mo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Design
Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (''de novo'' design) or by making calculated variants of a known protein structure and its sequence (termed ''protein redesign''). Rational protein design approaches make protein-sequence predictions that will fold to specific structures. These predicted sequences can then be validated experimentally through methods such as peptide synthesis, site-directed mutagenesis, or artificial gene synthesis. Rational protein design dates back to the mid-1970s. Recently, however, there were numerous examples of successful rational design of water-soluble and even transmembrane peptides and proteins, in part due to a better understanding of different factors contributing to protein structure stability and development of better computational methods. Overview and history The goal in ratio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Helix Bundle
A helix bundle is a small protein fold composed of several alpha helices that are usually nearly parallel or antiparallel to each other. Three-helix bundles Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains. The three-helix bundle in the villin headpiece domain is only 36 amino acids long and is a common subject of study in molecular dynamics simulations because its microsecond-scale folding time is within the timescales accessible to simulation. The 40-residue HIV accessory protein has a very similar fold and has also been the subject of extensive study. There is no general sequence motif associated with three-helix bundles, so they cannot necessarily be predicted from sequence alone. Three-helix bundles often occur in actin-binding proteins and in DNA-binding proteins. Four-helix bundles Four-helix bundles typically consist of four helices packed in a coiled-coil arrangement with a sterically close-packed hydrophobic core in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ColE1 Replication Control
ColE1 is a plasmid found in bacteria. Its name derives from the fact that it carries a gene for colicin E1 (the ''cea'' gene). It also codes for immunity from this product with the ''imm'' gene. In addition, the plasmid has a series of mobility (''mob'') genes. Its size and the presence of a single EcoRI recognition site caused it to be considered as a vector candidate. Replication ColE1 replication begins at the origin. 555 bp upstream from this point, RNA polymerase initiates transcription of RNAII which acts as a pre-primer and begins the synthesis of the leader strand. The transcript folds into a secondary structure which stabilises the interaction between the nascent RNA and the origin's DNA. This hybrid is attacked by RNase H, which cleaves the RNA strand, exposing a 3' hydroxyl group. This allows the extension of the leading strand by DNA polymerase I. Lagging strand synthesis is later initiated by a primase encoded by the host cell. Replication is carried out enti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
