Papers listed: Cell2 During the semester I will speak of information from several papers. For many of them you will not be required to read these papers, however, you can do so for the fun of it (and it may turn out being helpful). Some of these papers you will be required to read. I will make sure you know which ones they are. These papers can be found on Eres on the library website under my name or the course name (section 2). The password is Cell2. This weeks papers Stuart and Jones. (1997). Cutting complexity down to size. Nature. Vol. 386: 437-438. Roseman et al. (1996). The Chaperonin ATPase Cycle: Mechanism of allosteric switching and movements of substratebinding domains in GroEL. Cell. Vol. 87: 241-251. 1 2 and function The importance of proteins Major structural components of cells. Workers of the cell. See Panel 4-1. The functions of proteins are intimately related to their structures. and function An introductory example - the proteosome. (Stewart and Jones, 1977), 3 4 Chapt. 4. Protein Structure Chapt. 4. Protein Structure Proteins are composed of a linear sequence of amino acids joined by a peptide bond. This arrangement results in a backbone of N-CR-CO-N-CR-CO where the side groups (R) can have interesting chemistry (Fig. 4-1) 5 Fig. 4-1 6 1
Fig. 4-2 Proteins function not as linear strings but at as space filling structures. Therefore protein function is intimately related to protein structure. 7 Fig. 4.2 8 Interactions important in protein structure. The peptide bond Strong, covalent bond. Not readily reversible. Non-covalent bonds or interactions. Individually much weaker. Non-covalent bonds or interactions. Ionic 9 10 Fig. 4-4 Non-covalent bonds or interactions. Hydrogen (between 2 peptide bonds, between a side chain and a peptide bond, between aside chain and the backbone) 11 Fig. 4-4, Figure 3-26 from big Alberts 12 2
Non-covalent bonds or interactions. Van der Waals Non-covalent bonds or interactions. The hydrophobic interaction 13 Fig. 4-4b 14 Fig. 4-5 The importance of noncovalent bonds or interactions Proteins function not as linear strings but at as space filling structures. Therefore protein function is intimately related to protein structure. 15 Fig. 4-6 16 The primary structure of a protein is the linear arrangement of amino acids connected by covalent peptide bonds. 17 The secondary structure is one of two (or three) common patterns of short range interactions within or between the primary structure. In each case, the bonds involved are H bonds between the N and the O of the peptide bonds of the backbone --- side chains are not involved. 18 3
The a helix 19 Fig. 4-10 20 H bonds are within the chain and bond to the peptide bond of an amino acid 3.6 amino acids away. Fig. 4-10 The ß sheet (Fig 4.10) The ß sheet (Fig 5.10) H bonds are between chains. H bonds do not involve side groups 21 Fig. 4-10 22 Fig. 4-10 There are two types of ß sheets The tertiary structure is the arrangement of secondary structure and linking regions that results in a domain or a protein monomer. 23 Fig. 4-17 24 4
Fig. 4-19 Bonds involved in the tertiary structure include all kinds of non-covalent bonds, H bonds of multiple types, ionic bonds, van der Waals interactions, hydrophobic interactions. Side chains are frequently involved. 25 26 The quaternary structure is the arrangement of protein molecules into a larger structure. Fig. 4-22 Bonds involved include all kinds of noncovalent bonds, H bonds of multiple types, ionic bonds, van der Waals interactions, hydrophobic interactions. Side chains are frequently involved. 27 28 Similar looking proteins can be constructed very differently. Fig 4.20 Proteins fold into minimum energy conformations. The classic expt. that showed this. Fig 4-7 29 30 5
31 The challenge of determining protein structure. (see pgs 130-132) Primary structure fairly easy to determine from isolated protein. Primary structure is even easier to predict from the gene. However, much more difficult to determine how the primary structure is folded. 32 However, much more difficult to determine how the primary structure is folded. Experimental: Crystallize the protein Bombard with x-rays Interpret the diffraction pattern Computer analysis from primary sequence data. After all, folding simply is about forming the weak interactions such H bonds, ionic bonds etc. However it is difficult because there are a very large number of possible interactions to consider. Protein families. Fig. 4-21 Development of protein families. Gene duplication A to A and A Protein coded for by A can continue to do its job. However gene/protein A can undergo mutation and develop a new (but related) function. 33 34 An example: globin genes. An example: protein kinases. Human 35 36 6
Extracellular proteins are often stabilized by disulfide bridges (covalent cross-links) Fig. 4-29. The amino acid side chains (and to a lesser extent the backbone), contribute to the proteins chemistry (and thus function) 37 38 Small molecules tightly bound to proteins can play important roles in the function of the proteins. Fig. 4-36 Infectious misfolding can cause disease Prions mad-cow disease Creutzfeldt-Jakob disease (Fig 4-8) Chapt 4. Prions 39 retinal heme 40 41 Other protein folding diseases Abnormal protein folding can cause other diseases: Alzheimer s disease Extracellular protein aggregates Parkinson s disease Aggregation of proteins in nerve cells. Huntington s disease. Aggregation of proteins in nerve cells due to extra glutamine s inserted in primary structure. 42 The birth and death of proteins Synthesis and folding of proteins Some proteins selfassemble The molten globule (Fig. 4-28 from big Alberts) Molten globule Native (=folded) state 7
The birth and death of proteins Molecular chaperones The HSP-70 family of HSPs Fig. 6-83 from big Alberts History of chaperones and HSPs Importance and mechanism 43 44 The HSP-60 family of HSPs Fig. 6-84 from big Alberts 45 Alan M. Roseman, Shaoxia Chen, Helen White, Kerstin Braig, and Helen R. Saibil. 1996. The Chaperonin ATPase Cycle: Mechanism of Allosteric Switching and Movements of Substrate-Binding Domains in GroEL. Cell, Vol. 87, 241-251 46 The birth and death of proteins Degradation of proteins Why degrade proteins? The ubiquitin dependent pathway for protein degradation (Fig. 7-32) a) The proteosome. b) Ubiquitin (the tag) c) The overall process 47 48 8
Stewart, D. I. and E.Y. Jones. 1977. Cutting complexity down to size. Nature 386:437-438. 49 Stewart, D. I. and E.Y. Jones. 1977. Cutting complexity down to size. Nature 386:437-438. 50 Stewart, D. I. and E.Y. Jones. 1977. Cutting complexity down to size. Nature 386:437-438. 51 9