Biomolecular Interactions

Vakinformatie

Biomolecular Interactions

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G77AE.htm

Examenvragen

15 juni 2018

1. Robben: Wat zijn de verschillende manieren waarop EcoRV bindt met DNA, welke methodologieën om dit te onderzoeken?
2. Mizuno: Je collega ziet bij confocale microscopie dat membraaneiwit A en membraaneiwit B op de zelfde positie zichtbaar zijn en besluit dat ze dus interageren. Wat vind jij hiervan en waarom? Welke andere technieken zou je voorstellen en geef de achtergrond van deze technieken.
3. Van den Ende: polypeptide-polysaccharideinteracties voor ziektes: Geef belang aan met behulp van een voorbeeld, en geef een voorbeeld van hoe dit de basis zou kunnen zijn van een therapie.

26 juni 2017

1. Mizuno-senpai:
   1. 1) Explain the principle of the Scatchard plot using the degree of association (fi)

In notes. Actually all the rest too. 2) The two given plots depict a wild type (wt) and a mutant (cc) EGFR’s scatchard plot, with the twist that L(bound) is used instead of fi.

a) Explain, how to calculate the association constant! derive the linear, to get -K b) Give the association constant for CC! devide y intercept with x intercept, dont forget the unit! (K~0.9/12[1/pM]) c) What does the x intercept mean? We can read out E0, because fi=1 at the x intercept. fi=L(bound)/E0=1 → L(bound)=E0 d) Discuss the differences between WT & CC WT curves up, which indicates an additional binding site. As for that binding site, the association constant is greater (see graph) it has a higher affinity to the substrate. This binding site is lost in the mutation. (Also this is why it is conceptually incorrect to calculate K from the y intercept on the scatchard plot)

1. G. Maglia: Describe how DNA binding proteins recognize specific features in ssDNA and dsDNA.
2. J. Robben: You want to develop a new ELISA assay for Zika virus. The coat protein (the antigen) is

given. You decide to use phage display a) Describe how you would proceed in the lab! Procedure for antibody display (use nanobodies), biopanning, amplification etc. b) Which experimental measures would you use to ensure maximal afifnity? According to those, who had the oral with him, the answer was monovalent display (so type33 or type3+3 display)

1. J. Hofkens:

A new theory is proposed for the structure of biological membranes, according to which it contains: 1) Rafts 2) Compartments that are due to the partition of the actin filaments (cytoskeleton) in the membrane 3) Membrane proteins, that are present in oligomer form, or as transient dimers or bigger complexes. Describe how would you confirm this theory, with the microscopy techniques learned in class.

20/06/2016

1. Prof. Hideaki Mizuno Sensei : Single step reversible association and fast binding followed by a slower conformational change.
2. Prof. Robben : Describe by drawing diagram of genetic component of enzyme complementation system. What are the strengths and weaknesses of this system compare to the traditional transcription factor based system.
3. Prof. De Maeyer : Discuss pharmacophore modelling. Focus on module 2.
4. Prof.Hofkens : Imaging of receptor molecules in neural ring synapse in C.elegans.

20/08/2016

1. Prof. Hideaki Mizuno Sensei : Define the Binding equation. Derive the partition function and the association constant. Provide the Hill Plot and Scatchard plot of a single binding site. Explain what kind of information can be obtained from these plots. Explain the above analysis in the context of oxygen binding.
2. Prof. Robben : Give a schematic representation of Tandem Affinity purification. Explain why sometimes cross linking is used. How is the outcome of this experiment different from 2 hybrid systems..
3. Prof. De Maeyer : Discuss pharmacophore modelling. Focus on module 2(ligand receptor complex).
4. Prof.Hofkens : To distinguish the type of movement of two different motor proteins

21/08/2015

1. Prof. Hideaki Mizuno Sensei : Single step and two step binding kinetics models. Basically all the equations. Know about the rate constants, what do they mean and how do you obtain them. Does not give any equation or formula.
2. Prof. Giovanni Maglia : Explain how do proteins bind to a specific sequence in the major groove of the DNA.
3. Prof. Marc De Maeyer: Discuss pharmacophore modelling. Focus on module 3.
4. Prof. Johan Robben :· Classic yeast two-hybrid models are not viable if one or both proteins involved are cellular membrane proteins. Explain. · Give an example schematically on how would you model it correctly.