Protein Structure and Modeling

CHAPTER 1 - Protein Structure

1.1 Polypeptide chain

1.2 Ligand binding

1.3 Active site

1.3 Structure-function

CHAPTER 2 - Conformational transitions

2.1 Types of transitions in molecular systems

2.2 Conformational states

2.3 Quantum motions

2.4 Myoglobin and hemoglobin

2.5 Cytochromes

2.6 Tobacco mosaic virus coat protein

2.7 Fibrin-fibrinogen

2.8 Conformational changes of side chains in protein interior as a basis of the conformational states of the molecule

CHAPTER 3 – Allosteric regulation

3.1 Proteins

3.2 Nucleic acids

3.3 Small ligands

CHAPTER 4 – Protein channels

4.1 Structure-function

4.2 Signaling       

CHAPTER 5 - Helical assemblies

5.1 Determinants of specific helix recognition

5.2 Types of assemblies

CHAPTER 6 - multiprotein complexes

6.1 Postsynaptic density

6.2 Viruses

6.3 Implications in signaling

CHAPTER 7 - Methods of structure determination

7.1 X-Ray crystallography, NMR and Electron Microscopy

7.2 NMR

7.3 Electron Microscopy

CHAPTER 8 – Protein modeling

8.1 Helix and its interactions

8.2 Ligands

8.3 Dynamics

References

Dictionary