Nanostructured Biomacromolecules

Vakinformatie

Dit vak is een keuzevak in de opleiding master in de chemie. Het wordt gegeven door 3 professoren: professor Mizuno, professor Maglia en professor De Maeyer/professor Nies. De laatste twee wisselden elkaar af tot het academiejaar 2017-2018, professor de Maeyer ging op pensioen dus nam professor Nies zijn deel van het vak over.

Elke professor geeft tijdens dit vak 4 lessen over zijn onderwerp en op het einde zijn er presentaties die gegeven worden door jij en je medestudenten. Deze presentaties zijn per twee en de duo's worden door professor Mizuno onderverdeeld en zijn niet vrij te kiezen. Dit vak wordt ook nog gevolgd door de mensen uit de Erasmus mundi master van nanochemie dus meestal zal het samenwerken voor de presentatie met een van hen verlopen.

Professor Maglia geeft les over dynamische nanotechnologie en het gebruik van nanopores. Professor Mizuno geeft les over het cytoskelet, motor proteïnen en fluorescerende proteïnen. Professor Nies gaf voor 2017-2018 een deel over synthetische polymeren, maar gaf in het jaar 2017-2018 les over het computationeel modelleren van proteïne eigenschappen (is vgl met het vak computationele chemie uit de 3de bachelor chemie, maar dan veel minder wiskunde en een stuk interessanter les gegeven).

Beoordeling van dit vak gebeurt op meerdere criteria: - presentatie gegeven tijdens het semester - mondeling examen met schriftelijke voorbereiding (gesloten boek) met 1-2 vragen per professor (er kan niet bij elke professor mondeling verdedigd worden, hangt af van welke professor beschikbaar is op de examinering dag) - examinering van het deel van professor Nies bestond van het lezen van een paper over computationele modellering van proteïnen en deze linken aan de cursus + een paar korte vragen tijdens het mondelinge deel (dit was zo in het academiejaar 2017-2018, gelieve aan te passen indien zijn examinering anders verloopt)

Examenvragen

8 january 2026

Professor Rocha

Small questions: Describe briefly Ramachandran plot, cholesterol, and DNA origami Big questions: Describe and explain DNA strand displacement and design autonomous DNA walker

Professor Mizuno

Describe the machinery of muscle contraction and how myosin converts chemical energy into mechanical energy. Describe how the body can initiate muscle contraction and how the action potential passes through the system.

13 january 2022

Professor Maglia

Part A. Short (1/4 of page) description of the terms

1) Ramachandran plot 2) Stealth liposome 3) DNA origami

Part B

Principal of strand displacemen. AND or OR logic gate.

Professor Nies

Part A. NpT ensemble. 1) How it is called, 2) Which variables are fixed, which can be measured and 3) How control over fixed variables is realized

Part B. Examples and discussion of non-bonded and bonded forces in MD.

Professor Mizuno

Muscle contraction, including function of myosin and T-tubules.

29 januari 2018

Oral examination by professor Nies

Professor Maglia

1) Basic principle of double strand displacement and design AND gate on the basis of given inputs

Professor Mizuno

1) Explain mechanism and regulations of muscle contraction

17 januari 2018

Oral examination by professor Nies

Professor Maglia

Dynamic DNA nanotechnology by strand displacement: 1) describe the basic principle 2) design an AND gate and by-product by using the DNA strand depicted below

Input A: 1*2*3* Input B : 3 4 5

Output C: 4 6 5

this is normally an example given in the course slides

Professor Mizuno

Describe the molecular mechanism of anterograde vesicle transport along the microtubules in cells

Terms: alpha tubulin/ beta tubulin, relay helix, neck linker, kinesin P-loop and ATPase

12 january 2018

Oral exam with Prof Mizuno or Prof Nies if you completed his assignment.

Prof Mizuno

1. Describe how calcium is involved in muscle contraction.
2. Oral questions on the details of calcium transport and the exact channels used

Prof Nies

1. General structure of an amino acid
2. Discuss the surfaces used in molecular simulations
3. What conditions are controlled and observed in canonical ensemble setup for MD simulations?

Prof Maglia

1. How are nanopores used for sequencing

8 January 2016

Prof Marc De Mayer

1.Give the full charge (non polar) Amino Acids. influence your choice?

2.How can we obtain thermal stabilization in proteins and DNA ? <<< it was about using Dead end elimination theory and eliminate some rotamers, also asked in oral to show that on the graph of rotamers energy.

Prof Mizuno

Explain every thing you know about Muscle Contraction / Myosin, and plot as much as you can. and some terms to be clarified during your answer like ( P-loop, Sarcomer, T-tubules......etc).

Prof Maglia Giovani

Chose one of the following questions:

1.2D and 3D strutures question. principle and application.

2.DNA Strand Displacement. principle, applications.

3.Explain a Re configurable self assembly structure. << this is a part of the paper of Strand displacement.

26 January 2015

Oral parts by prof. De Maeyer and prof. Mizuno

Prof. Maglia

One of both: 1.Dynamic DNA nanotechnology by strand displacement: basic principle, examples and applications. 2.Nanopores can be used to sense molecules.

Describe: the basic principle nanopore sensing what and how analytes can be detected with nanopores limitations and how to overcome such limitations

Prof. Nies

Question 1

Explain the following concepts and defenitions: 1. Δmixg</math> 2. coexistence curve 3. spinodal 4. critical state 5. LCST

Figure 1 gives a graphical presentation of Δmixg. Discuss how one can "see" and/or determine the different definitions (b-e) in graphical presentations such as in Figure 1. To support your discussion, you can make use of more typical graphical presentations like that in Figure 1.

Question 2

A monodispers polystyrene (PS) has a molar mass M = 480kg/mol. The molecular formula of PS is -(CH2-CH(C6H5))n- and the chemical structure can be written as figure of structure - calculate the contour length - calculate the unperturbed average quadratic end-to-end distance and radius of gyration of the PS molecule - calculate the number of Kuhn segments and the Kuhn length of the polystyrene chain.

Some data: C-C bond length = 0.154nm, C-C-C bond angle θ = 109° molar mass C = 12g/mol, molar mass H = 1g/mol, C∞=9.8

Prof. Mizuno

Describe how myosin and kinesin convert the chemical energy to the mechanical energy. What are roles of the P-loop and the relay helix? Give an example of biological phenomenon using respective motor proteins and explain. The answer should be understandable for layperson, and use schematic drawings.

Prof. De Maeyer

1.You retrieve the coordinates of a PDB-protein structure from the databank. How would you evaluate if the model is OK? Enumerate as many tests that you could think off, to do such an evaluation and clarify why these criteria are valid. You may want to use the formularium.

2.X-ray protein structures from the PDB do not always contain all the atom positions. Sometimes some of the side-chains are not solved in the electron density. How could you optimise these side-chains atom-coordinates after sprouting the missing atom-coordinates?

Januari 2014

Prof de Maeyer

How do you characterize H-bonds and Salt bridges in Force Fields(formularium given)? Discuss H bonds in more detail Give the polar non charged amino acids

Prof Mizuno

A certain process (forgot name) is used to carry cargo radially to the edge of a cell, discuss how this can happen (obviously Kinesin on Micro-Tubuli). Use the words neck linker, relay helix, dynamic instability, P-loop, Centromere, etc.

Prof Nies

Given an formula for Flam and Fhom, determine the condition for Chi*N for the transition (Basic math). Give a formula of Chi in function of N. What does the Gibs free energy of mixing of a solution of a polymer in solvent look like, in function of the volume fraction of polymers? Given the global volume fraction and the volume fractions of the different phases. Discuss the interesting properties of the graph (Mainly binodal and spinodal points).

Prof Maglia (answer 1 out of 2 questions)

Explain nanopore sequencing (Different technologies, how to detect a base, issues, solutions) Explain Dynamic DNA nanotechnology

January 2013

Prof de Maeyer

Salt bridges are charge-charge interactions. Where in a protein would you put them to stabilise it (formularium given)? Give the aromatic hydrophobic amino acids

Prof Mizuno

Explain the principle behind kinesin movement on microtubuli.

Prof Nies

Question about polymer calculations (cf exercise session) Calculate the dependence of diblock polymer long period length on parameters

Prof Maglia (answer 1 out of 2 questions)

Explain nanopores

Explain protein technology