Biophysics Laboratory for 2nd Level

physics

Biophysics Laboratory for the II degree studies; compulsory for studies in molecular biophysics as a specialization in physics. The required competence is the same as that which allows students to start the II degree studies in the respective fields. Participating students will be made familiar with some advanced methods of molecular biophysics.

Blended learning

Biophysics Laboratory for the second Level is composed of two parts. In the first part, students participate in seven one-day workshops devoted to particular methods of molecular biophysics. In the second part, students select two methods for four weeks of laboratories.

In the first part of the Biophysics Laboratory for the Second Level, the following methods will be discussed

1. mass spectrometry of proteins and peptides

2. molecular dynamics simulations of biomolecules

3. application of bio-layer interferometry (BLI) for real-time monitoring of biomolecular interactions.

4. surface plasmon resonance and intermolecular interactions

5. investigtion of protein-ligand interactions using microscale thermophoresis

6. protein interactions studied by quartz crystal microbalance

7. methods of electrophysiology of biological membranes

In the second part, each student participates in two four-week laboratories devoted to chosen two methods for closer studies, chosen by students.

1. Kevin M. Downard a and Simin D. Maleknia, Mass spectrometry in structural proteomics: The case for radical probe protein footprinting, Trends in Analytical Chemistry 110 (2019) 293-302

2. B. Miedziak et al., Kinetic analysis of IFIT1 and IFIT5 interactions with different native and engineered RNAs and its consequences for designing mRNA-based therapeutics, RNA, 26 (2020) 58-68;

3. Motohiro Tagaya, In situ QCM-D study of nano-bio interfaces

with enhanced biocompatibility, Polymer Journal (2015) 47, 599-608;

4. A. Hollingsworth and R. O. Dror, Molecular Dynamics Simulation for All, Neuron, vol. 99, no. 6, pp. 1129–1143;

5. Electrophysiological characterization of membrane transport proteins,

Grewer, C., et al., Annual Review of Biophysics, 42, pp. 95–120, 2013

6. Jerabek-Willemsen M. et al. MicroScale Thermophoresis: Interaction analysis and beyond. Journal of Molecular Structure (2014), 1077, 101-113

7. Xiao-Li Zhou, Yunze Yang, Shaopeng Wang and Xian-Wei Liuunze, Surface Plasmon Resonance Microscopy: From Single-Molecule Sensing to Single-Cell Imaging, Angew. Chem. Int. Ed. 2020, 59, 1776-1785;

The student upon completing the laboratory

1. Learned new or deepened the knowledge of known methods of molecular biophysics, both at an advanced level;

and is able to:

2. plan a simple physical experiment in collaboration with a tutor

3. build and test a simple experimental set-up unaidedly

4. complete the measurements in collaboration with a tutor

5. analyse the experimental data

6. write a report on the exercise

The exercises will be graded by the persons responsible for them. The final grade will be a weighted average of the grades from individual

exercises.

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