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It allows us to find where secondary structural elements ( α helices, β sheets, loops) are located. Secondary Structure Predictors Chou-Fasman COMBINE GORIII PRISM PHD0 PHD3 PSIPred PSIPred uses most recent algorithm that can predict secondary structure of about 80% accuracy. Protein Threading or Protein Fold Recognition Although proteins are of large no, tertiary structural motifs are limited to which most protein belongs. It is speculated that about 1000 distinct protein folding patterns may be present in total. Surprisingly, a few dozen folding patterns account for about half of all known protein structures . This helps to use previously solved structures as starting point. To identify the fold the sequence is compared with all 500+ folds in library of known protein structure . If pair-wise alignment shows less than or nearly 30% identity then it is ideal to be used for protein fold recognitions. When successful, structure from fold recognition may be about 3-6Å RMSD (root mean...

Why prediction of protein structure important ? You may ask what is there in protein structure?? That is because structure determines function of the protein. Take the example of enzyme dehydrogenases. It has an NAD-binding site called Rossaman fold ( Dinucleotide binding fold). This fold is made up a pair of βαβαβ subunit. Thus if a protein contain a βαβαβ subunit than it acts as a binding site for a nucleotide . Structure is better conserved than sequences in protein during the course of evolution e.g. take the example of Cytochrome C of eukaryotes and C-cytochromes of prokaryotes in different species(which change with evolution in prokaryotes) where all perform general functions i.e. electron carrier. But different species exibit low degree of similarity of sequence to each other and to that of eukaryotes. They also differ in polypeptide loops on surface . But X-Ray structure are similar particularly chain folds and side chain packing to interior . We require structural knowl...

Have you ever asked a question that if restriction enzyme could ingest invading viral DNA then why don't it destroy cell's own DNA ???? Reason behind it that all restriction enzyme are paired with methylases that recognize and methylate restriction DNA sites. After methylation, DNA site(e.g. GAATTC in case of EcoRI) are protected against most restriction endonucleases. The two enzymes: Restriction endonuclease and methylase are collectively called Restriction-Modification system or R-M System . But what about newly synthesized strand that will be unmethylated just after replication?? How does it protect it self from its own restriction enzymes?? In this case every time the cellular DNA replicates, one strand of the daughter duplex will be a newly made strand and will be unmethylated. But the other will be a parental strand and therefore be methylated. This half-methylation (hemimethylation ) is enough to protect the DNA duplex against cleavage by the great majority of res...

Let us first define what comparative genomics actually mean . It is practice of analyzing and comparing genetic material of different species for purpose of studying functions of genes , studying evolution and inherited diseases . But why do we require comparative genomics ? What is importance of it? It tells us what are unique and common between different species at genome level . E.g. To identify unique crucial protein in pathogens to use as targets for products that are both safe and effective. Genome comparison is surest and most reliable way to indentify genes , predict their functions and interactions . E.g. To distinguish between orthologues and paralogues. Here we have two new terms: Orthologues and Paralogues . Actually genes with similar sequence are called homologous genes . These genes may undergo gene duplication or even get divergent in functions during the course of evolution. Genes with similar sequence and functions are called orthologues and genes with sim...

Chain Termination Method (Sanger et al 1977) In this method sequence of single stranded DNA molecule determined. This is done by enzymatic synthesis of complementary polynucleotide chain. These chains terminate at specific nucleotide positions. Principle Single stranded DNA differing in length by single nucleotide can be separated by polyacrylamine gel electrophoresis . So we can get lengths from 10 to 1500 nucleotide into series of bands. Steps Starting material is identical s ingle s tranded DNA molecule. Then short oligonucleotide is annealed to each single stranded molecule at same position . These gonucleotide acts as primer . Strand synthesis requires DNA polymerase , dNTPs (Deoxyribonuleotide triphosphate) as substrate. The DNA synthesis doesn't continue for long because along with dNTPs small amount of ddNTPs ( Dideoxyribonucleotide triphosphate – It lacks 3'-hydroxyl group need to form connection with next nucleotide) is added . The polymerase can't discri...

Sample Preparation Hundreds and thousands of copies of single cell type is made from which protein can be extracted. Get Cell: Cell of single type is grown, obtained from biopsy or body fluids Culture Cell: Cells are then placed in growth medium in petridish. Cells feed and multiply. Now base of the petridish is covered with thousands of cells . Make More Copies: Cells are again divided in more petridishes to get more copies of cells. Millions of copies are produced. Then the cells are scraped from petridish base and put it in test tube Add Detergent: Detergent added ruptures outer membrane of cell membrane. Now the test tube contains proteins along with cell debris . Spin: The solution is know centrifuged to separate proteins form cell debris like cell membrane, cytoskeleton. After centrifugation the test tube contains cell debris at bottom and protein above . Separation A single cell has millions of protein type. Hence there separation is necessary. 2D Electrophoresis: ...

A virus has helped to create a new type of tiny battery , made with a simple stamping technique that could power miniature devices . Electronic devices used for controlled drug delivery , or to power tiny lab-on-a-chip applications , need to get their power from somewhere. But as conventional batteries are made smaller and smaller, they contain less and less of the materials that actually store charge, causing a decline in efficiency . Using nanoscale components can boost a battery's capacity to store charge. Now, scientists at the Massachusetts Institute of Technology, Cambridge, have designed a quick method to build a microbattery that relies on a genetically-engineered virus called M13. The scientists first made a template from polydimethylsiloxane (PDMS), a commonly used silicon-based organic polymer. After coating it with alternating layers of positive and negative electrolytes , they added the virus . The virus had been designed to have negatively charged amino aci...

Do you know? The first human chromosome to be sequenced is chromosome no 22. The sequencing completed in December 1999 The genetic code of it comprised of 33.5 million bases About Chromosome 22 Chromosome 22 is the second smallest of the human autosomes. The short arm (22p) contains a series of tandem repeat structures including the array of genes that encode the structural RNAs of the ribosomes , and is highly similar to the short arms of chromosomes 13, 14, 15 and 21. The long arm (22q) is the portion of human chromosome 22 that contains the protein coding genes and this is the region that has now been sequenced. The completed sequence consisted of 12 contiguous segments covering 33.4 million bps separated by 11 gaps of known size. One of these gaps has subsequenctly been closed by the Oklahoma group. The sequence is estimated to cover 97% of 22q, and is complete to the limits of currently available reagents and methodologies. The largest contiguous contig is >23 million bps...