Genetic Engineering : Structural Genome

Structural Genome :

  By definition, structural genomics aims to determine the structure of the gene product or the protein sequence by combining experimental and predictive modeling approaches.  Although used as a loose term in man’ cases, field of structural genomics include determination of macromolcular structure, study of homology within and across species and determination of possible funtion of the structure. Starting point of structural gcnomics is the raw sequence dat.i generated through sequencing projects. Assignment of structures to the sequenced nucleotide fragment can be performed in two principal s’ays. One direct
method is to translate the sequence in vain providing necessary Inputs for RNA and protein synthesis and sequence the protein product usingpn fromk pprrodrcs, Thesecond ism siiicvpredictiom of the protein structure from the sequence using bfcnjbnnatk approtrlws based on the homology with other known protein
structures and predictive three dimensional configurations of amino acids in a polypeptide chaiit In the first method, protein structures may be determined by sequencing based approaches. spectrometric approaches or by crystallography, In computational biomatics approach. homoglobin are detected by sequence
comparison and algorithms are used to detect homolglobin. recognition of possible structural domains and building of models of three dimensional structures, Structure determination can also be used as a tool for studying species and evolutionary relationships, because similarity in structure of proteins is well conserved across species. Many a times changes in protein structures have led to differentiation in evolutionary pathways. Dilferences in structur are not only observed between species, but also within species at population levels. Wide variation in haemioglobin structure can be observed in human population that
stems up from sequence difference and three dimensional configurations of the interlinked peptide chains. Irnmunoglobuline. on the other hand show high variation within the body itself, although there are specific conserved motifs shared by all immunoglobulins. Such homologies are esploited extensively to
determine funciionality of a new protein identified by matching its sequence with the known proteins.

      A structural genomics project should first fix the target protein for investigation. Because there are several proteins expressed in the cell1 proteins that are crucial to the cellular processes such as metabolic proteins, or DNA modifying proteins have been given more emphasis. Several studies have also targeted to structural determination of proteins that are expressed in particular tissue or in response to environmental conditions or stresses. One of the important components in target selection is identification of domains that may possibly be presentn in the protein. For example homeobox proteins share a common homeodomain or the topoisomerases have common ‘TopRim’ domain. If the target protein falls under this group, these domains should be present in the protein. Search for availability of such sequence can be made in the protein! DNA data banks maintained in National Centre ft,r Biolecimology Information (NCBI) or Protein
Information Resources (PIR). If related sequence is not available, sequences may be derived from cloning and characterizing DNA sequences from genomic libraries or EST databases by screening with appropriate primer combinations. If the protein is to be identified in r’itro, cell free extracts can be used to direct the
synthesis of protein from the sequence. This is followed by purification of the protein by fractionation, separation by electrophoretic processes and ultimate structure determination through proteomics using spectrometric, crystallographic or direct sequencing approaches. As a gene may give rise to many possible
protein products through post transcriptional and post transnational modifications, direct structure determination from cell free synthesized protein is advantageous over computational based predictions or in iitro synthetic translation.