Biocrystallography - TEORIA (2009/2010)

Course partially running

Course code
4S00160
Name of lecturer
Ugo Luigi Monaco
Number of ECTS credits allocated
5
Academic sector
BIO/11 - MOLECULAR BIOLOGY
Language of instruction
Italian
Location
VERONA
Period
2nd Semester dal Mar 1, 2010 al Jun 15, 2010.

To show the organization of the course that includes this module, follow this link * Course organization

Lesson timetable

2nd Semester
Day Time Type Place Note
Wednesday 8:30 AM - 10:30 AM lesson Lecture Hall L  
Thursday 8:30 AM - 10:30 AM lesson Lecture Hall L  

Learning outcomes

The goal of the Biocrystallography course for the degreee in Molecular and Industrial Biotechnology is to develop in the student the skills necessary to critically read and assess scientific papers in this branch of science which is central in modern Structural Biology.
After an introduction to the fundamentals of the theory of diffraction and the modern methods of data collection a detailed discussion of the phase problem is undertaken, along with the methods used to solve it for small molecules as well as macromolecules. During the course papers selected from the current literature dealing with important biological structures are read and discussed in detail. The laboratory introduces the student to the basic experimental techniques of the field, in particular those concerning the preparation of biological crystals.

Syllabus

Introduction. Methods used to determine the three-dimensional structure of macromolecules. The role of Biocrystallography in macromolecular Structural Biology.

The theory of X-ray diffraction. Geometry of an X-ray scattering experiment. Scattering of a single electron and an atom. The atomic scattering factor. Structure factor. The structure factor of atoms not located at the origin. The diffraction pattern of a one-dimensional array of atoms. X-ray diffraction from a three-dimensional array of atoms. The von Laue scattering conditions. The structure factor of a crystal. Fourier transforms. Convolutions and their use in the computation of structure factors. Bragg’s law of diffraction.

Properties of crystals. Symmetry. Symmetry elements. Space groups. Reciprocal lattice. Preparation of macromolecular crystals. Properties of protein crystals. The relationship between the crystal lattice and the reciprocal lattice. The Ewald sphere. Determination of the space group and of the number of molecules in the unit cell of a macromolecular crystal.

Determination of the molecular structure by X-ray crystallography. The phase problem. Steps in determining the structure of a macromolecule. X-ray sources. Data collection methods. Solving the phase problem. The method of multiple isomorphous replacement. The Patterson function. Treatment of errors. Computation of electron density maps. Molecular replacement. Other methods used to solve the phase problem.

Model building and refinement. Interpretation of the electron density maps. Building the model. Refinement methods. Assessing the model quality. The R factor. Ramachandran plots. Checking the stereochemistry.

Some important results of Biocrystallography. Using the Fourier difference synthesis to study the function of proteins. Conformational changes. Time resolved Biocrystallography. The importance of synchrotron radiation.

Recommended Textbooks

!) Rupp, B. (2010) Biomolecular Crystallography. Garland Science, New York

2) Giacovazzo, C. (Editor) (2000) Fundamentals of Crystallography. Second Edition Oxford University Press, Oxford.
3) Blow, D.( 2005) Outline of Crystallography for Biologists Oxford University Press, Oxford.

4) Blundell, T. L. & Johnson, L. N. (1976) Protein Crystallography. Academic Press, New York.

5) Drenth, J (1994) Principles of Protein X-ray Crystallography. Springer Verlag.

6) Cantor, C. R. & Schimmel, P. R. (1980) Biophysical Chemistry Volume 2. W. H. Freeman and Company, San Francisco.

7) McPherson, A. (1983) The Preparation and Analysis of Protein Crystals. John Wiley, New York.

Assessment methods and criteria

oral

Studying