Figure 5-1

Table 5-1

Figure 5-4

Page 97

Figure 5-5

Table 5-2

Figure 5-6

Figure 5-7

Figure 5-8

VVP Fug, 5-8 Purification of Stapylococcal Nuclease

Stryer Fig. 4.7 PAGE

Stryer Fig. 4.8

Page 106

Animation

Stryer Fig. 4.9 Coomassie blue stained SDS gel.

Figure 5-9

Figure 5-10

Figure 5-11

Figure 5-12

Box 5-1

Figure 5-13

Page 107

Table 5-3

Figure 5-14

Figure 5-14 part 3

Figure 5-15

Figure 5-16a

Figure 5-16b

Figure 5-18

Figure 5-19

Amino acid Models from Cal LutheranModels

See VVP Fig 4-3

VVP Fig 6-3 p 126

Example of a protein sequence MANSKINKQL DKLPENLRLN GRTPSGKLRS FVCEVCTRAF ARQEHLKRHY RSHTNEKPYP CGLCNRCFTR RDLLIRHAQK IDSGNLGETI SHTKKVSRTI TKARKNSASS VKFQTPTYGT PDNGGSGGTV LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ SHATKHKIPI KYLEFISEAI IHVLHSRHPG DFGADAQGAM NKALELFRKD IAAKYKELGY G N-terminus C-terminus

N-termini C-termini VVP Fig 5-1 p 94

Other Properties of Amino Acids Stereochemistry (all biosynthetic proteins made up of L-isomer) Hydropathy (partitioning between polar and nonpolar solvents as indicator of polarity) (see Table 6-2 in VVP p 150) these two properties are major determinants of peptide conformation

VVP page 150 “nonpolar” “polar”

Figure 6-1 part 4

Protein Data Bank Workshop pdb Rasmol Do the protein explorer tour!!!!! beta/pe/protexpl/qtour.htm

Chapter 6 Opener

Figure 6-4

Figure 6-5

Figure 6-6

Figure 6-7

Figure 6-8

Figure 6-9

Figure 6-9a

Figure 6-9b

Figure 6-10

VVP Fig 6-16 pdb

Table 6-1

Figure 6-12

Figure 6-15 Keratin: a coiled coil

Figure 6-16 Higher order keratin structure

Globular Protein 3 o Structure 2 o structural elements (helices, sheets, turns…) pack together to give a folded protein or subunit. This so-called “tertiary” structure is stabilized by non- covalent interactions, the hydrophobic effect and disulfides. Within the 3 o structure are “motifs” and “domains”. The 3 o structure can be derived from one or more domains.

Figure 6-20b Protein crystals: flavodoxin

Figure 6-20e Protein crystals: lamprey hemoglobin

Figure 6-21

Figure 6-27 cytochrome c: hydrophillic residues and hydrophobic residues

Figure 6-33 Hemoglobin

Table 6-3

Figure 6-35 Bovine chymotrypsin

Figure 6-38 Molecular dynamics of Mb

Page 159

Figure 6-39

Figure 6-40

Figure 6-41

Many conformational states Fewer conformational states A “single” conformational state Low energy High energy (Fig 6-38)

Many conformational states Fewer conformational states A “single” conformational state See VVP Fig 6-37 p153

“Ideal” “Real” ? See VVP Fig 6-38 p154

H-bond Fun Fact 1984 survey of protein crystal data shows that “almost all groups capable of forming H-bonds do so.” (mainchain amides, polar sidechains)

Table 6-4

Figure 5-3