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<p>We describe protein folding patterns according to a hierachy of primarym secondary, tertiary and quaternaty sturctures</p>
<p>Domains / Modular proteins / Polypeptide chain / mainchain / sidechains / primary structure / hydrogen bod / secondary structure / alpha helix / beta sheet / folding pattern / tertiary structure / quantenary structure / native state / denaturant / denatured state / post-translational modification / disulphide bridge </p>
<p> </p>
<p>-Why is there a common genetic code with 20 canorical amino acids?</p>
<p>Level of transcription </p>
<p>Formation of different splice variants </p>
<p>mRNA editing </p>
<p>the nature and binding sites of ligands integral to the final sturcture </p>
<p>post translational modifications </p>
<p> </p>
<p><span style="color:#0000CD"><strong>Seperation and anylsis of proteins </strong></span></p>
<p>All methods of separating molecules require two things</p>
<p>1. A difference in some physical property, between the molecules to be separated</p>
<p>2. A mechanism taking advantage of that property, to set the molecules in motion, the speed differing according to the value of the property selected. This moves apart molecules with different properties. </p>
<p> </p>
<p>To measure an inventory of the proteins in a sample, the proteins must be 1. separated 2. identified. 3. counted </p>
<p>-Polyacrylamide gel electrophoresis (PAGE)</p>
<p>> SDS (Sodium Dodecyl Sulphate) - PAGE</p>
<p>-Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE)</p>
<p>> Isoelectric point / isoelectric focusing </p>
<p>-Mass spectrometry</p>
<p>> Rapid identification of the components of a complex mixture of proteins </p>
<p>> sequencing of proteins and nucleic acids</p>
<p>> Anaylsis of post-translational modifications or substitutions relative to an expected sequence</p>
<p>> Measuring extents of hydrogen deuterium exchange to reavel the solvent exposure of individual sites </p>
<p>> Mass spectrometry is oftern used to characerize proteins isolated from mixtures. The peptide mass fingerprint is usually sufficiennt to identify a protein </p>
<p> </p>
<p><span style="color:#0000CD"><strong>Classification of protein structures</strong></span></p>
<p>-SCOP</p>
<p>> Strucutural Classification of Proteins) offers facilities for searching on ketwords to identify structures, navigation up and down the hierarchy, generation of pictures, access to the annotaion records in the PDB entries and links to related databases. </p>
<p> </p>
<p>-Changes in folding patterns in protein evolution</p>
<p> </p>
<p><span style="color:#0000CD"><strong>Many proteins change conformation as part of the mechanism of their function</strong></span></p>
<p>Many proteins are microscopic machines, with internal parts moving in precise ways to support their function </p>
<p>By their nature, transition states are reactive and difficult to trap long enough for structure determination. Possible solutions include enzymes binding transition -state analogues or inhibitors, or lowering the temperature to slow down the reaction </p>
<p> </p>
<p>-Conformational change during enzymatic catalysis</p>
<p>-Motor proteins</p>
<p>Myosins /Kinesins / Dyneins /Linear motors / rotary motor. / sarcomere</p>
<p>-Allosteric regulation of protein function</p>
<p>> Allosteric proteins deviate from the michaelis -menten curve in ligand binding or in the cases of allosteric enzymes, in reaction velocity as a function of substrate concentration. The cooperativitiy is achieved by ligation - induced conformational change. </p>
<p> </p>
<p>-Conformational states of serine protease inhibitors (serpins)</p>
<p>The differnce in colour between arterial and venous blood reveals the different state iron in ligated and unligated hemoglobin.</p> <p> </p> <p><span style="color:#0000CD"><strong>P</strong></span><span style="color:#0000CD"><strong>Protein rotein structure prediction and modelling</strong></span></p>
<p>-Homology modelling</p>
<p>> is one of the most useful techniques for protein structure prediction - when it is applicable </p>
<p>Attempts to predict secondary structure </p>
<p>Fold recognition</p>
<p>Prediction of novel folds </p>
<p> </p>
<p>-Available protocols for protein structure prediction</p>
<p>-Structural genomics</p>
<p>Critical Assessment of Structure Prediction (CASP) </p>
<p>CASP categories change as the field progresses. Secondary structure prediction and fold recognition have been discontinued. Prediction of residue- residue contacts of disordered regions and the ability to refine models have been added. </p>
<p> </p>
<p> </p>
<p><span style="color:#0000CD"><strong>Directed evolution and protein design</strong></span></p>
<p>-Directed evolution of subtilisin E</p>
<p>Artificial selection and evolution / natural selection</p>
<p>-Enzyme design</p>
<p> <span style="color:#0000CD"/p> <strongp>Protein complexes and aggregates<The procedure of directed evolution comprises these steps></strongp> </spanp>1. Create variant genes by mutagenesis or genetic recombination</p>
<p>-Protein aggregation diseases2. Create a library of variants by transfecting the genes into individual bacterial cells.</p>
<p>-Properties of protein-protein complexes3. Grow colonies from the cells and screen for desiable properties.</p>
<p>-Multisubinit proteins4. Isolate the genes from the selected colonies and use the as input to step 1 of the next cycle.</p>
