Explain briefly how you can use a dotplot to compare two genomes and identify regions that are found in just one of the genomes.

 


  1. Explain briefly how you can use a dotplot to compare two genomes and identify regions that are found in just one of the genomes. (5 p)
  2. It turns out that these proteins are expressed at increased temperature. Explain how you can use 2D gel electrophoresis and mass spectrometry to identify these proteins. (10 p)
  3. You assume that the genes for these proteins are activated by a known temperaturesensitive transcription factor. This factor recognizes a motif in DNA which can be represented by the sequence logo shown in Figure 1. Explain what we mean by a PSSM

(position-specific scoring matrix) or PWM (position weight matrix), how a sequence logo can be made from a PSSM/PWM, and what the logo in Figure 1 tells us about the binding motif. You do not need to use formulas. (10 p)

Figur 1 – Sekvenslogo / Figure 1 – Sequence logo

 

Mange av de patogene egenskapene til Listeria examinensis ser ut til å være knyttet til de proteinene som uttrykkes ved økt temperatur. Du vil derfor predikere viktige egenskaper for disse proteinene.

  1. Et av proteinene lager en kanal i cellemembranen. Det er to hovedtyper av proteinstrukturer som lager slike transmembrane kanaler. Beskriv kort de to hovedtypene, og hvordan du kan predikere hvilken hovedtype ditt protein tilhører. Forklar hvordan du kan predikere en transmembran region i proteinet ved hjelp av for eksempel hydrofobisitet.

Forklar hva som menes med en amfifatisk heliks. (10 p)

  1. Et annet protein har en lang α-heliks som er viktig for protein-protein interaksjoner ved å danne en coiled-coil struktur. Forklar hvordan en slik struktur ser ut, og hvilke interaksjoner eller egenskaper vi bruker for prediksjon av coiled-coil regioner. (5 p)
  2. Mange metoder for prediksjon av sekundærstruktur er basert på neurale nettverk. Beskriv hvordan et typisk nettverk for prediksjon av sekundærstruktur ser ut. Forklar hvordan vi vanligvis koder proteinsekvenser som input til et neuralt nettverk, og hvilke kategorier av sekundærstruktur et slikt nettverk vanligvis predikerer. Forklar hvordan doble nettverk

(sekvens til struktur og struktur til struktur) fungerer. (10 p)

Problem 4 – Protein properties (25 p)

Many of the pathogenic properties of Listeria examinensis seem to be linked to the proteins that are expressed at increased temperature. Therefore you want to predict important properties for these proteins.

  1. One protein makes a channel in the cell membrane. There are two main types of protein structures that make such transmembrane channels. Describe briefly the two main types, and explain how you can predict which main type your protein belongs to. Explain how you can predict a transmembrane region in the protein using for example hydrophobicity.

Explain what we mean by an amphipathic helix. (10 p)

  1. Another protein has a long α-helix which is important for protein-protein interactions by forming a coiled-coil structure. Explain what such a structure looks like, and which interactions or properties we use to predict coiled-coil regions. (5 p)
  2. Many methods for prediction of secondary structure are based on neural networks. Describe what a typical network for prediction of secondary structure looks like. Explain how we normally code protein sequences as input to a neural network, and which categories of secondary structure such a network normally predicts. Explain how double networks (sequence to structure and structure to structure) work. (10 p)
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