Sequence-function

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

Computer hardware and software used in 2DLC generally take care of three critical operations. These include real-time control of valves and sequencing functions such as autosampler control, formatting the time series data into a 2D data matrix, and analyzing the data. These will be described in some detail. 

Roman, M. et al., Immunostimulatory DNA sequences function as T helper-1-promoting... 

The history of molecular biology has been a history of technological developments for determining the primary and tertiary structures of protein and nucleic acid molecules. Once the molecular structure is known, it provides clues to molecular functions. This is the principle of the structure-function relationship. Based on this principle the analysis of the amino acid sequence is performed to decipher the functional information from the sequence information. The analysis usually involves detection and prediction of empirical sequence—function relationships with additional consideration of known or predicted three-dimensional (3D) structures. Thus, the process can be represented schematically as ... 

Genes are considered here as the basic elements (building blocks) that constitute a living organism (system). A traditional strategy to establish the structure—function (or sequence—function) relationship of... 

Fox, R.J. and. Huisman, G.W., Enzyme optimization moving from blind evolution to statistical exploration of sequence-function space. Trends Biotechnol, 2008, 26, 132-138. 

Hard FU, Hlodan R, Langer T (1994) Molecular chaperones in protein folding the art of avoiding sticky situations. Trends Biochem Sci 19 20-25 Hausler T, Stierhof YD, Blattner J, Clayton C (1997) Conservation of mitochondrial targeting sequence function in mitochondrial and hydrogenosomal proteins from the early-branching eukaryotes Crithidia, Trypanosoma and Trichomonas. Eur J Cell Biol 73 240-251... 

Termination Eventually, the two replication forks of the circular E. coli chromosome meet at a terminus region containing multiple copies of a 20 bp sequence called Ter (for terminus) (Fig. 25-17a). The Ter sequences are arranged on the chromosome to create a sort of trap that a replication fork can enter but cannot leave. The Ter sequences function as binding sites for a protein called Tus (terminus utilization substance). The Tus-Ter complex can arrest a replication fork from only one direction. Only one Tus-Ter complex functions per replication cycle—the complex first encountered by either... 

With an automated control system, verifying the sequencing functions may be appropriate during the OQ testing. The first step is verifying the interfaces to the field devices, such as pumps, motors, and valves, and their proper operation. This should include operation of proportional control valves. 

Roman, M., Martin-Orozco, E., Goodman, J.S., Nguyen, M.D., Sato, Y., Ronaghy, A. etal. (1997) Immunostimulatory DNA sequences function as T helper-1-promoting adjuvants. Nat. Med., 3, 849-854. 

Schlosser, K., Gu, J., Sule, L., and Li, Y. (2008a). Sequence-function relationships provide new insight into the cleavage site selectivity of the 8—17 RNA-cleaving deoxyribozyme. Nucleic Acids Res. 36, 1472-1481. 

Fig. 1 Blocks of multiple sequence alignment of protein sequences of carboxypeptidases from B. taurus, Mus musculus, Rattus norvegicus, Neurospora crassa, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens along with protein sequence from H. pylori (Uniprot accession code HPAG1 0372 from strain HPAG1). Numbers on the top correspond to amino acid residue number of the carboxypeptidase enzyme from B. taurus. Gray vertical columns indicate conserved residues. Amino acid residues corresponding to Glu-182 and His-306, which coordinate to zinc, are conserved, whereas another Zn-coordinating amino acid residue corresponding to His-179 is substituted by Gin in the Helicobacter sequence. Functionally important residues corresponding to Arg-237 are also conserved...

Goffin, V., Shiverick, K. T., Kelly, P. A., and Martial, J. A. (1996). Sequence-function relationships within the expanding family of prolactin, growth hormone, placental lactogen, and related proteins in mammals. Endocrine Reviews 17, 385—410. 

There are three ecdysone receptor isoforms ECR-A, ECR-Bl, and ECR-B2. All have identical DBDs and LBDs, but differ in the amino-terminal sequences. Functional... 

The RCSB P06 provides a variety of tools and resources foi studying the structures of blologicat macromolecules and their relationships to sequence, function, and disease. 

Prokaryotes use two means for terminating transcription, factor-independent and factor-dependent. Certain DNA sequences function as signals that tell the RNA polymerase to terminate transcription. The DNA of a terminator sequence encoded an inverted repeat and an adjacent stretch of uracils. Factor-dependent termination involves a terminator sequence as well as a factor or protein called rho. The mechanisms by which eukaryotes terminate transcription are poorly understood. Most eukaryotic genes are transcribed for upto several thousand base pairs beyond the actual end of the gene. The excess RNA is then cleaved from the transcript when the RNA is processed into its mature form. 

Introduction Classification Occurrence and Sequences Functional Role X-Ray Crystal Structures... 

Shealy RT, Murphy AD, Ramarathnam R, Jakobsson E, Subramaniam S. Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure. Biophys J 2003 84 2929 12. 

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