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BYU BIO 465 - Protein Structure Prediction

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Slide 1Why do we want to know protein structure?What is protein structure?Primary StructureSecondary StructureSecondary StructureSecondary StructureClassificationMore ClassificationProtein Structure ReviewSecondary-Structure Prediction ProgramsTertiary StructureTertiary StructureQuaternary StructuresStructure DisplaysSoftwareClassic Approach to Determining Structure?Structural Genomics Approach?Sources of Protein Structure Information?Structural PredictionComputational ModelingHomology ModelingSlide 233D Comparative ModelingStructural HMMProtein Structure PredictionWhy do we want to know protein structure?ClassificationFunctional PredictionWhat is protein structure?Primary - chains of amino acidsSecondary - interaction between groups of amino acidsTertiary - the organization in three dimensions of all the atoms in a polypeptideQuaternary - the conformation assumed by a multimeric proteinProteins are chains of amino acids joined by peptide bondsThe N-C-C sequence is repeated throughout the protein, forming the backbone The bonds on each side of the C atom are free to rotate within spatial constrains,the angles of these bonds determine the conformation of the protein backbone The R side chains also play an important structural rolePolypeptide chainThe structure of two amid acidsPrimary StructureInteractions that occur between the C=O and N-H groups on amino acidsMuch of the protein core comprises  helices and  sheets, folded into a three-dimensional configuration:- regular patterns of H bonds are formed between neighboring amino acids- the amino acids have similar angles- the formation of these structures neutralizes the polar groups on each amino acid- the secondary structures are tightly packed in a hydrophobic environment- Each R side group has a limited volume to occupy and a limited number of interactions with other R side groups  helix sheetSecondary Structure helix sheetSecondary StructureOther Secondary structure elements(no standardized classification)- loop- random coil- others (e.g. 310 helix, -hairpin, paperclip) Super-secondary structure- In addition to secondary structure elements that apply to all proteins (e.g. helix, sheet) there are some simple structural motifs in some proteins - These super-secondary structures (e.g. transmembrane domains, coiled coils, helix-turn-helix, signal peptides) can give important hints about protein functionSecondary StructureStructural classification of proteins (SCOP)Class 1: mainly alpha Class 4: few secondary structures Class 2: mainly beta Class 3: alpha/beta ClassificationAlternative SCOPClass  : only  helices Class  : antiparallel  sheets Class / : mainly  sheetswith intervening  helices Class + : mainlysegregated  helices withantiparallel  sheetsMembrane structure:hydrophobic  helices withmembrane bilayers Multidomain: containmore than one class More ClassificationQ: If we have all the Psi and Phi angles in a protein, do we then have enough information to describe the 3-D structure?Tertiary structureA: No, because the detailed packing of the amino acid side chains is not revealed from this information. However, the Psi and Phi angles do determine the entire secondary structure of a proteinProtein Structure ReviewSecondary-Structure Prediction Programs * PSI-pred * JPRED Consensus prediction (includes many of the methods given below) * DSC * PREDATOR * PHD * ZPRED * nnPredict * BMERC PSA * SSPThe tertiary structure describes the organization in three dimensions of all the atoms in the polypeptideThe tertiary structure is determined by a combination of different types of bonding (covalent bonds, ionic bonds, h-bonding, hydrophobic interactions, Van der Waal’s forces) between the side chains Many of these bonds are very week and easy to break, but hundreds or thousands working together give the protein structure great stabilityIf a protein consists of only one polypeptide chain, this level then describes the complete structureTertiary StructureProteins can be divided into two general classes based on their tertiary structure:- Fibrous proteins have elongated structure with the polypeptide chains arranged in long strands. This class of proteins serves as major structural component of cells Examples: silk, keratin, collagen- Globular proteins have more compact, often irregular structures. This class of proteins includes most enzymes and most proteins involved in gene expression and regulationTertiary StructureThe quaternary structure defines the conformation assumed by a multimeric protein.The individual polypeptide chains that make up a multimeric protein are often referred toas protein subunits. Subunits are joined by ionic, H and hydrophobic interactionsExample:Haemoglobin(4 subunits)Quaternary StructuresCommon displays are (among others) cartoon, spacefill, and backbone cartoonspacefillbackboneStructure DisplaysSoftwareRasMolCn3DJmol (Chime)Classic Approach to Determining Structure?Determine biochemicaland cellularrole of proteinPurify proteinExperimentally determine3D structureClone cDNAencodingproteinObtain proteinBy expressionInfer function, mechanism of actionStructural Genomics Approach?genomicDNA sequencespredictprotein-codinggenesObtain proteinby expressionObtain proteinIn silicoExperimentallydetermine3D structurePredict 3D structureDeterminebiochemical andcellular roleof proteinhomology searches (PSI-BLAST)3-D macromolecular structures stored in databases The most important database: the Protein Data Bank (PDB)The PDB is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB) and can be accessed at three different sites (plus a number of mirror sites outside the USA):- http://rcsb.rutgers.edu/pdb (Rutgers University)- http://www.rcsb.org/pdb/ (San Diego Supercomputer Center)- http://tcsb.nist.gov/pdb/ (National Institute for Standards and Technology)It is the very first “bioinformatics” database ever buildSources of Protein Structure Information?Researches have been working for decades to develop procedures for predicting protein structure that are not so time consuming and not hindered by size and solubility constrains.As protein sequences are encoded in DNA, in principle, it should therefore be possible to translate a gene sequence into an amino acid sequence, and topredict the three-dimensional structure of the


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BYU BIO 465 - Protein Structure Prediction

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