Lecture_2_5513_2005

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1 Structural genomics BINF 5513 Lecture 2

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2 What is Structural bioinformatics? Part of bioinformatics that focuses on the analysis of folding of polynucleotide and polypeptide chains and organizing knowledge in databases

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3 What is Structural Genomics or Structural bioinformatics? Structural genomics is the assignment of three-dimensional structures to the complete protein repertoire and the investigation of their biological implications. Protein structure is an important indicator of function, Two levels of assignment are employed in structural bioinformatics, 1. experimental large-scale determination of protein structures using NMR or X-ray crystallography, 2. computational structure prediction usually through detection of homologies with proteins of known structure.

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4 Why structural information is important? Biology bases on structural observation. Molecular biology bases on structural observation as well. Example: Discovery of DNA double helices structure helps us to understand the mechanism of the 'central dogma' or the mechanism of the information transfer : DNA  RNA  Protein  Function 1. Home assignment What protein functions do you know

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5 Where does structural biology currently stand ? We understand most of the basic principles of protein, RNA and DNA structure. Detailed DNA structure ? We have atomic structures for many of the important classes of proteins. We have atomic structures of many of the key types of RNA.

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6 I. Goals of structural bioinformatics: Creation of methods for Prediction of a structure from a sequence and visualization

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7 Terminology Primary structure - the sequence of amino acid residues MESSTHEDRKVLDL … Three one-letter abbreviations Met Glu Ser Ser Thr His… one-letter abbreviations Home assignment Present all amino acids in three and one-letter alphabets.

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8 Secondary structure H: helix (alpha,) E: extended (beta strand) C: coil (i.e. anything else) For example: one helix, one beta strand and three loops Primary: MSEGEDDFPRKRTPWCFDDEHMC Secondary: CCHHHHHHCCCCEEEEEECCCCC

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9 Tertiary structure The full 3D structure of a single peptide chain Secondary structure elements pack together to form a structural core Loops tend to lie on the protein surface Called a protein “fold”

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10 Quarternary structure How several fully folded protein chains pack together to form a fully functional protein.

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11 What happens if proteins don't fold correctly? Diseases such as Alzheimer's disease, cystic fibrosis, Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding. When proteins misfold, then can clump together ("aggregate"). These clumps can often gather in the brain, where it is believed to cause the symptoms of Mad Cow or Alzheimer's disease.

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12 II. Goals of structural bioinformatics: Creation of methods for Comparison of structures, Prediction of function from structure, Prediction of intermolecular interactions docking, drug discovery Docking - Computational exploration of the possible binding modes of a ligand to an enzyme, receptor, or DNA. Drug - A molecule used to diagnose, treat, mitigate, or prevent disease. Drug discovery - Processes for the the identification and development of drugs.

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13 Proteins assemble themselves to do their work. This self-assembly is called "folding." C. Anfinsen discovered the main rule of the structural biology: All information about the native structure of a protein is coded in the amino acid sequence. 2. Home assignment Explain how you understand the rule.

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14 Chaperones assist in protein folding After release from ribosomes, most protein chains fold spontaneously into their final 3D structure. Protein folding is driven by the need to shelter hydrophobic and carbon-rich regions from the surrounding water. But large proteins or proteins with several domains are assisted by chaperones. (Goodsell, 2002)

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15 The hierarchical description of protein structure Primary structure (amino acid sequence) Secondary structure is defined by the strands and helices. Tertiary structure shows how a single polypeptide chain form a three-dimensional structure. Quaternary structure describes how two or more polypeptide chains form a native protein structure (but some proteins consist of a single chain).

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16 Amino acids The 20 amino acids were found within proteins. Basic Structure All amino acids found in proteins have this basic structure, differing only in the structure of the R-group or the side chain.

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17 diagram showing the relationship of the 20 naturally occurring amino acids to a selection of physio-chemical properties thought to be important in the determination of protein structure 3.Home assignment Show the structures of all 20 amino acids.

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18 Essential amino acids Humans can produce 10 of the 20 amino acids. (alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine and tyrosine). The others must be supplied in the food. Failure to obtain enough of even 1 of the 10 essential amino acids, those that we cannot make, results in degradation of the body's proteins—muscle and so forth.

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19 the peptide bond forms between the carbon atom (C) of the carboxyl group and the nitrogen atom (N) of the amino group. Next step tripeptide and so forth … polypeptide

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20 PROTEIN GEOMETRY. A diagram showing the bond angles, bond lengths and general geometry of a peptide bond. Bond angles are given in degrees.

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21 PROTEIN GEOMETRY. Planes formed on the two sides of an Alpha Carbon and Angles of Rotation of Peptide. Omega to 180 degrees in very nearly all of the main chain peptide bonds psi phi Rotations around Ca- C and N-Ca bonds give a lot different conformations. Question: all phi and psi angle values are allowed? Try to answer before you look at next slide.

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22 Answer : From physic we know that atoms repulse if they come close to each other. (They repulse at a distance 2-3 Å). So, in polypeptide chains the torsion angles phi and psi are not free to rotate. To determine allowed values of the torsion angles phi and psi, Ramachandran used computer models of small polypeptides to systematically vary phi and psi. For each conformation, the structure was examined for close contacts between atoms

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23 The red regions correspond to conformations where there are no steric clashes, i.e. the allowed regions namely the alpha-helical and beta-sheet conformations. The white areas correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radi. These regions are sterically disallowed for all amino acids The yellow areas show the allowed regions if slightly shorter van der Waals radi are used in the calculation, i.e. the atoms are allowed to come a little closer together.

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24 Hydrogen bond – is one of the most important type of attractive force. (Remember nucleotide pair in DNA – Watson-Crick pair) Hydrogen bond exists between two atoms with opposite polarity. As the name "hydrogen bond" implies that the bond involves a Hydrogen atom. the positive hydrogen to be positioned between two negative atoms The energy of a hydrogen bond lies in between the energies of covalent bonds and van der Waals interactions, and is of the order of 2-10 kcal mol-1

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25 Unlike van der Waals interaction, H-bonding is orientation sensitive. O not more O - H ---------- than 20-30º The orientation sensitive properties is very important for strict molecular recognition? Question: Try to answer why it is so important

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26 The specific backbone Torsion Angles phi and psi and specific main chain Hydrogen Bond pairings results in Secondary Structure 3. Home assignment Explain and show the hydrogen bond between main chain atoms

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27 The hierarchical description of protein structure Primary structure (amino acid sequence) Secondary structure is defined by the strands and helices. Tertiary structure shows how a single polypeptide chain form a three-dimensional structure. Quaternary structure describes how two or more polypeptide chains form a native protein structure (but some proteins consist of a single chain).

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28 Secondary structure in protein characterize a repeating values of phi and psi along the chain, which result in regular structures. There are two types of regular structure : Alpha-helix and Beta-strand For example, repeating values of phi ~-57º and psi ~-47º give a right-handed helical fold (the alpha-helix).

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29 Alpha helix is held together by intrachain H-bonds which along the same region of the backbone of the polypeptide chain. Water is excluded from the inner core of the alpha helix, which is very hydrophobic. 4. Home assignment: Give a list of residues which can be in the core. Hint: define hydrophobic residues

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30 phi(deg) psi(deg) H-bond pattern ------------------------------------------------------------------ right-handed alpha-helix -57.8 -47.0 i+4 pi-helix -57.1 -69.7 i+5 310 helix -74.0 -4.0 i+3 (omega is 180 deg in all cases) ----------------------------------------------------------------- From http://www.imb-jena.de It may be little different parameters of angles and consequently slightly different helices

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31 Hydrogen bonds occur at regular intervals along an alpha helix, Hydrogen bonds provide an effective stabilizing force only when many act together, as they do here. Why does the peptide remain in a helical shape? Two important interactions occur to stabilize helical folding: 1. Hydrogen bonds form between the backbone oxygens and nitrogens. A set of hydrogen bonds gives Right-Handed Alpha-Helix 2. Hydrophobic interactions are another source of stability. The helix folds so as to minimize the contact of hydrophobic carbons with the watery medium.

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32 Beta SHEET are also held together by hydrogen bonds. But they are called inter chain H-bonds since they form between two parts of the polypeptide backbone separated from one another by some distance or length of the amino acid sequence of the polypeptide. Two types of backbone chain order is found: 1. ANTI-PARALLEL where chains run in the opposite direction 2. PARALLEL where the chains run in the same direction

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33 5.Home assignment Find the difference of Hydrogen bonds in parallel and antiparallel chains. antiparallel parallel chains.

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34 Why secondary structure assignment from structure is important Indicative of protein 3D fold Useful conceptualization for understanding structure Influences the sequence alignment It is related to function It is useful as part of structure prediction – defines regions on the templates

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35 How to assigns every residue to a secondary structure state. The most famous is a program DSSP - Dictionary of Protein Secondary Structure“. The main idea secondary structure recognition algorithm based mainly on H-bonding patterns. Why? - ~90% of backbone donors (NH) and acceptors (C=O) form hydrogen bonds. On average, about half of the residues in proteins are located in helices and sheets.

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36 PDBsum: A database of the known 3D structures of proteins and nucleic acids Helix strand

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37 Home assignment Describe PDBSUM database and make power point presentation