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| Detailed information |
| Original study plan |
Master's programme Joint Master Programme Biological Chemistry 2010W |
| Objectives |
(*)Introduction to crystallography as one of the most important methods of determining molecular structures. Why study molecular structures, structure – function relationships in chemistry and biology.
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| Subject |
(*)Experimental setup, crystal growth, sources of radiation (x-ray lamps, synchrotron etc.)
Data collection and reduction. Crystallographic symmetry
Structure determination. Solution of the „phase problem“
Reflections, electron densities and Fourier transforms
Structure refinement. Improvement of the molecular model
Validation and analysis of structures
Comparison of crystallography to other experimental methods as electron microscopy, NMR, and other spectral methods, and to methods of computer simulations by quantum mechanics and methods of empirical potential (molecular dynamics).
Finding structures: Structural databases. Practical introduction to the most important databases CSD (for organic molecules) and PDB (the primary repository for 3-D macromolecular structures). Other internet databases important for structural biology. mmCIF and other formats used for archiving structures
Comparing structures by tools of structural bioinformatics. Stereochemistry of the building blocks of biomolecules, amino acids and nucleotides. Sequence alignments, relationship between amino acid sequence and protein structure and fold. Methods of structure comparisons.
Structural motives of the protein secondary structure, tertiary structure motives, classifications of protein folds.
Structures of nucleic acids. I. Helical conformations. II. 3D folding of RNA and DNA.
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| Criteria for evaluation |
(*)Oral examination
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| Methods |
(*)Lectures, demonstrations
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| Language |
English |
| Changing subject? |
No |
| Further information |
(*)Recommended reading:
G. Rhodes: Crystallography made crystal clear. Elsevier, Amsterdam (2006).
J.P. Glusker; M. Lewis; M. Rossi: Crystal Structure Analysis for Chemists and Biologists. VCH, New York (1994).
J. Drenth: Principles of protein x-ray crystallography. Springer, New York (1994).
C. Brandén & J. Tooze: Introduction to Protein Structure. Second Edition, Garland, New York (1998).
S. Neidle: Nucleic acid structure and recognition, Oxford University, Oxford (2002).
J. Gu & P.E. Bourne: Structural Bioinformatics. Second Edition, Wiley-Blackwell, Hoboken (2009)
A.M. Lesk: Introduction to Bioinformatics. Oxford University, Oxford (2002).
B. Alberts; A. Johnson; J. Lewis; M. Raff; K. Roberts; P. Walter: Molecular Biology of the Cell, Garland, New York (2002).
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