Protein secondary structure: Analysis and prediction

11Hartley, J R and Lovell, K (1977) 'The Psychological Principles Underlying the Design of Computer-Based Instructional Systems', in Computer Based Science Instruction (Edited by A Jones and H Weinstoek), Noordhoff International, Groningen 12Laurillard, D M (1978) 'The Design of Interactions in CAL Packages', Computers in HigherEducation Conference, Lancaster, p 224 13Newman, W M and Sproull, R F (1979) Principles oflnteractive Computer Graphics, Second Edition, McGraw-Hill,New York and London, pp 239-245 14Lewell, J (1983) 'The Dollar Guide to Computer Graphics. Part 3 Plotters, Printers, and Photographic Recorders', Audio VisualDirections 5(1), 42-45 1SGorter' V (1983) 'The Art of Graphics Photography', Comp Systems 37-40 l~;Bryce, C F A and Stewart, A M (1982) 'Computer-Based Activities in Biochemistry; Avee Teeth, Avee Eyes, Avec Taste, Avec Everything, Biochem Microcomp GroupNewslett 7, 2-10 17Guilford' j (1959) 'Three Faces of Intellect', Am Psychol 14,469-479 PROTEIN SECONDARY STRUCTURE: ANAL YSIS AND PREDICTION R C HIDER and S J HODGES

Department of Chemistry U n i v e r s i t y o f Essex C o l c h e s t e r CO4 3SQ, U K Introduction

Of the three major classes of biological molecules, nucleic acids, polysaccharides and proteins, the latter adopt the greatest variety of structural types and yet, it is only in recent years that the principles underlying protein construction have become increasingly clear. They may adopt elongated fibre-like structures, as in collagen and keratin, they may form water-soluble globular structures capable of conformation changes, or they may adopt appreciable hydrophobic character as is found in the intrinsic membrane proteins involved in redox reactions and transport phenomena. Proteins may form large oligomeric structures such as fatty acid synthetase or ferritin, some proteins have molecular weights well over 100 000, for example immunoglobins and the membrane-bound spectrin, while others, for instance cobra-venom toxins consist of just 60 amino acids. It is the intention of this experiment to give an insight into how the higher protein structural orders can be predicted from an amino acid sequence. Future reference to proteins in this article is limited to soluble 'globular' molecules, which have the majority of the hydrophobic amino acid residues located in the interior of the protein, while hydrophilic residues are located largely on the outer surface. It is stressed that the principles outlined may not be applicable to other protein classes, eg membrane-bound proteins. Since LinderstrSm-Lang and Schellman ~ defmed four types of protein structural hierarchy; primary, secondary, tertiary and quaternary structure, two more levels of organisation have been added, both of which assist the definition of the tertiary structure. These are (i) supersecondary structure, which describes the relative orientation of secondary structural units, and (ii) domains, which can be considered as parts of a protein forming well-defined globular structures. Domains are usually limited to between 50 and 250 amino acid residues.2 The secondary structure of proteins can be separated into three major types; 'helical', '/3sheet', and 'reverse turn'. There are two known types of helical structure; the relatively abundant a-helix and the less commonly observed 31 o-helix, which is only found as short segments. Both these structures are right-handed. As indicated by its abundance, the a-helix is a relatively stable form of secondary structure with hydrogen bonds running parallel to the direction of propagation of the helix. A minimum of four successive residues is required to make one turn. Proline is of particular interest with respect to a-helices in that it is rarely found in a position other than the first turn of a helix and thus is usually thought of as a non-helical amino acid residue. The/~-sheet structures are termed parallel and antiparallel depending on the relative direction of the composite polypeptide strands. When two strands of a protein backbone are running in opposite directions, they are considered to form a unit of antiparallel ~-sheet, the reverse being true for parallel/~-sheet. Most/~-sheet structures are non-planar having a left.handed twist enabling them to pack tightly to units of a-helix. The third major class of secondary structure is the reverse turn, which is generally associated with a sharp reversal in the direction of the polypeptide backbone. Most reverse turns are located on the surface of proteins and consequently contain mainly hydrophilic residues. Overlapping/~turns can generate a 3t ohelix.

B I O C H E M I C A L E D U C A T I O N 12(1) 1 9 8 4

10 Since the 1950-60 period when Sangera elucidated the sequence of insulin, and Kendrew4 discovered the three-dimensional structure of myoglobin, an enormous number of protein sequences and three-dimensional structures have been reported, s A protein of given amino acid sequence always forms the same three-dimensional structure, but the mechanism by which this folding process occurs is not known. It is known, however, that protein folding is remarkably efficient. Consider a protein of 100 amino acid residues; if as a first approximation it is assumed that there are three stable backbone conformations at each a-carbon and for each side-chain there are three stable conformers, then the total number of possible conformations for this protein is 91 oo. If it is also assumed that each molecular arrangement takes 10-13 seconds, then the time necessary to sample all the possible conformations would be 1073 years. In practice, however, proteins refold in 10-1 to 103 seconds. The efficiency of this process is further highlighted by studies with cystine-containing proteins, for example ribonuclease, which has four disulphide bridges. There are 105 possible arrangements of the four cystine crosslinks. However as demonstrated by Anfmsen, rib6nuclease rapidly refolds in high yield to a single native conformation. 6 Clearly the folding process of proteins to their native state cannot be a random process. Indeed, the efficient folding of many small proteins has led to the concept o f nucleation centres. These centres are thought to consist of segnents of a-helix and elements of hydrogen-bonded/3-sheet. Evidence has been presented that supports the concept of the polypeptide chain collapsing to a globular structure with the hydrophobic side chains orientated away from the aqueous phase, followed by the nucleation of secondary structure. 7 In contrast, others believe that the nucleation centres form initially and that these subsequently orientate themselves with each other forming the native three-dimensional structure. 8 Irrespective of which concept is correct, the conclusion that the secondary structure, and thereby the tertiary structure, of a protein, is somehow coded in the sequence appears inevitable. Thus, in principle, it should be possible to predict the secondary structure that a sequence of amino acids would adopt and thereby derive the tertiary structure. 2 With the elucidation of a large number of protein primary and tertiary structures, various structural predictive methods have been developed which can be classified as being either probabilistic or physico-chemical in nature. An excellent review of protein prediction methods has been made by Schultz and Schirmer. 9 A stereochemical method developed for the prediction of ct-helical units covering a hydrophobic core was developed by Schiffer and Edmundson. 1o It was shown that if the residues constituting such a helix were drawn on a wheel with 18 equallyspaced spokes, such that adjacent residues are separated by 5 spokes (ie 3.6 residues per turn) then the non-polar residues were found to be associated with an arc of the wheel. The wheel represents the view along the axis of the helix and is an extremely useful technique for identifying amphiphilic helices. The underlying principles of the probabilistic methods is that if a particular amino acid has a structural preference, for example if it prefers an a-helical conformation, a survey of proteins of known sequence and three-dimensional structure should identify this structural preference. A widely adopted method based on such analysis is that developed by Chou and Fasman 11 who calculated, for each amino acid, structural propensities for a-helix,/3-sheet and positional propensities for reverse turns. Subsequently Levitt 12 made a similar analysis and as his parameters are drawn from a larger data-base they are adopted in this experiment. The calculation for the structural propensities of glutamate, using Levitt data, is shown in Table 1, and the complete set of parameters as developed by Levitt are shown in Table 2. Methodology

Having selected a series of parameters, there are a number of ways in which they can be applied to locate regions of preferred secondary structural tendencies. Chou and Fasman developed a series of rules for such analyses. In their method they analysed overlapping hexapeptide segments, eg i--1 to/-I-4, i to i+5, i+1 to i+6, ere, in an attempt to locate clusters of at least four helix-favouring residues while simultaneously containing not more than one helix-breaking residue. Similarly, pentapeptide segments were searched for clusters of/3-sheet-favouring residues. In regions where there is contention between the allocation of different structural types, as is often the case, the arithmetic means for the amino acid parameters in each of the predicted structural blocks are compared, bias being given to the larger value. Having thus decided on possible nucleation centres, the units of predicted structure are extended in both directions such that tetrapeptides are taken and the mean parameter value is calculated. If this value is greater than the threshold, the residue that was added is included in the predicted segment. This process is re-

B I O C H E M I C A L E D U C A T I O N 12(1 ) 1984

11

Table I

The derivation o f the structural propensities o f glutamate for a-helix, Pod ~-sheet, P~" and reverse turn, Pr; using Levitt data. 12 Number of Residues

Residues in s-Helix

Residues in O-sheet

Residues in Reverse Turn

282 5507

126 1715

59 1555

57 1121

Glutamate All Amino Acids

Number of Glutamate residues in given structure Total number of Glutamate residues

Frequency of occurrence of Glutamate in a structure,

Hence,

fa

Glutamate

0.477

Frequency of occurrence of any amino acid residue in a structure, fli Hence

=

f~

fr

0.209

0.202

Number of amino acids in structure Total number of amino acids

:)r

J)c~

All Amino Acids

0.311

0.282

0.204

Therefore the probability of occurrence of Glutamate in a particular structure is given by the formula: Pi =~-TI Thus,

1.44

Glutamate

0.74

0.99

peated until the mean tetrapeptide value falls below the threshold. Tetrapeptide units are also analysed for reverse-turn potential. As there is a marked preference for some amino acid residues to occupy particular positions in a reverse turn, the parameters depend on the position in the turn (Fig. 1). Although this method has gained wide acceptance for the identification of helical, sheet and reverse turn sections, a problem often encountered is that a number of predicted structures are frequently possible. In an attempt to minimise such ambiguity, Dufton and Hider, 13 while still adopting the search distances of 6, 5 and 4 for a-helix,/~-sheet and reverse turn, analysed polypeptide sequences by using the product of the structural parameters. It is this approach that is adopted in the experiments here. A typical application of the method is shown in Table 3 where a theoretical peptide is analysed. It can be seen that a-helix is predicted for the segment 6-12,/~-sheet for

R

B3

(~ ~o - ' ' %

Figure I

Glycine Proline

Prl

Pra

Pr3

Pr4

1.23 1.36

1.01 3.42

2.05 0.59

1.78 0.77

A diagrammatic representation o f a Type I reverse turn and the reverse turn positional propensities for proline and glyeine as found by Chou and Fasman.l 4 These data are based on 457 reverse turns in 29 proteins

BIOCHEMICAL EDUCATION 12(1) 1984

12 Table 2

The s-helix, ~-sheet and reverse turn propensities as developed by Levitt. 12 Values greater than unity indicate a greater than average tendency for the amino acid residue to adopt the structure concerned. This data is based on 66 proteins grouped into 31 classes. It can be seen that amino acid residues that have branched side chains, eg valine and isoleucine tend to be found in [J-sheet, while amino acids with side chains that are non-branched at the ~-carbon, such as glutamate and methionine tend to be found in or-helices. Amino acids with short hydrophilic side chains, eg serine and asparagine, tend to be found in reverse turn conformation. Amino Acid

Pa

P[J

P'c

Alanine Cystine Leucine Methionine Glutamate Glutamine Histidine Lysine

A C L M E Q H K

1.29 1.11 1.30 1.47 1.44 1.27 1.22 1.23

0.90 0.74 1.02 0.97 0.75 0.80 1.08 0.77

0.77 0.81 0.58 0.41 0.99 0.98 0.68 0.96

Helicalpreferring

Valine Isoleucine Phenylalanine Tyrosine Tryptophan Threonine

V I F Y W T

0.91 0.97 1.07 0.72 0.99 0.82

1.49 1.45 1.32 1.25 1.14 1.21

0.47 0.51 0.59 1.05 0.76 1.04

Sheetpreferring

Glycine Setine Aspartate Asparagine Proline

G S D N P

0.56 0.82 1.04 0.90 0.52

0.92 0.95 0.72 0.76 0.64

1.64 1.32 1.41 1.28 1.91

Arginine

R

0.96

0.99

0.88

Reverse turnpreferring

segments 1 - 5 and 7 - 1 2 with a single reverse turn prediction, centred on the dipeptide segment 6 - 7 . That the product of the Pa values for segment 6 - 1 2 is markedly lower than that of the P[J values for the segment 7 - 1 2 favours the [j-sheet prediction. Thus the predicted structure contains antiparallel [j-sheeted segments 1-5 and 8 - 1 2 connected by a reverse turn (Fig. 2). This particular example shows an idealised prediction and such clear analyses are not always found in practice. Consider the following examples using protein segments of known primary and tertiary structure.

H

I

1

0 Carbon

Figure 2

•

Nitrogen

•

Oxygen

Diagramr~ztic representation of the ~-sheetpredicted from the sequence of amino acids shown in Table 3. The solid black line represents the peptide backbone, o, carbon;., nitrogen, and •, oxygen

BIOCHEMICAL EDUCATION 12(1) 1984

13

Table 3

The calculated structural tendencies for ~-helix Pa ; ~-sheet, P#; and reverse turn, Pr ; for a theoretical sequence o f amino acid residues using the mathematical methodology o f Dufton and Hiderl S and Levitt parameters.12 i + 5 sig-aifiesthe product o f six ad]acent Pa values IIPa i

1 V

R

F

H

5 P

N

L

0.53

0.76

0.83

0.75

0.75

L04

1.23

Amino Acid

D

10 H

I

Y

F

i+5

.1]' Pa

a helix i+4

II

i+3 II i

Examples of Method

,-rl~ ~J

1.35

0.17

PI"

0.69 0.71 /3 sheet

0.39

0.67

0.96

0.98

0.52

0.87

1.44

1.86 ~ sheet

2.00 0.53 0.28 ~ Reverse turn

0.51

0.21

Helical Protein Segments Lysozyme The calculated structural probabilities for the N-terminal segment of lysozyme are shown in Table 4. This segment is known to possess a unit of a-helix over residues 4 - 1 5 . It is clear that u-helix is the dominant structure predicted over residues 3 - 1 5 , with the/~-sheet tendency being dwarfed by very strong helical values. Similarly, the product of the reverse turn parameters for residues 4 - 7 is of insufficient magnitude for it to compete with the a-helix potential. Conversely, the reverse turn predictions for residues 16-22 does dominate the C-terminus of this segment. Only the phenylalanine residue at position 3 is incorrectly predicted to be in the ahelix. If a helical wheel is constructed (see Introduction) of all the residues found in the observed a-helix (Fig. 3) then the amphiphilic character of the structure can be seen.

Table 4 The calculated structural tendencies for a-helix, ~-sheet and reverse turn for the N-terminal 22 amino acids o f lysozyme (chicken)

Amino Acid i+5

II i

i

V

F

G

5 R

C

E

L

A

10 A

A

M

K

R

15 H

G

L

D

N

20 Y

Pa

0.71 0.84 1.19 1.44 3.324.46 5.91 5.05 3.73 3.52 1.53 1.54 1.09 0.80 0.60 0.47 0.47 ~, helix

P~

0.76 1.11 1.14 0.52 0.50 0.46 0.56 0.72 0.54 0.60 0.72 0.74 0.77 0.72 0.56 0.64 0.69 0.62 /3 sheet

PI"

0.89 0.72 0.70 1.16 0.41 0.36 0.34 0.26 0.19 0.23 0.27 0.24 0.96 0.58 0.93 1.75 1.12 1.70 1.98 reverse turn ~ ~ reverse turn

i+4

II

1 K

R

G

i+3

II i

Calcium-binding Protein The results obtained from the analysis of the two a-helical units in the N-terminal region of Carp muscle calcium-binding protein (Fig. 4) show a more typical analysis (Table 5), that is, one possessing several interpretations. The tendency for the entire sequence is towards a-helix, with some high values over the 2 - 1 5 segment. In contrast only low values are found for #-sheet search. However, long a-helices are uncommon in proteins (Fig. 5) and thus it is unlikely that the predicted 26 amino acid segment will be in an a-helical conformation, but rather, in two shorter lengths. Where the a-helical tendency is at a minimum there is a turn prediction; thus if a break occurs in the identified helical unit it would most probably reside at resi-

BIOCHEMICAL EDUCATION 12(1) 1984

14

'

A

G

ca!

~oncharged H ~ surface

Figure 3 Helical wheel o f observed N-terminal a-helix o f lysozyme

Table 5

Figure 4 A diagrammatic representation o f the three dimensional structure o f carp muscle calcium binding protein. The section under analysis is highlighted

The calculated structural tendencies for the two a-helical units at the N-terminus o f carp muscle calcium binding protein (Figure 4) 5

Amino Acid

N

D

A

D

2.25

2.79

2.82

0.51

0.61

0.76

0.76

1.96

0.78

0.43

0.43

10

I

A

A

A

L

E

A

C

K

i+5

l-I Pct

1.57

i

~

3.90

5.18

4.46 4.25 t~-helix

4.25

4.22

3.05

1.94

1.87

1.08

0.56

0.56 0.46 #-sheet

0.39

0.35

0.42

0.33

0.43

0.23

0.26

0.34

0.36

0.59

0.46

0.46

0.80

i+4

1-1 ~ i

"P

.4

~-

i+3

II i

/'r

~

15 A

0.34

turn

20 H

K

A

1.99 1.99 a-helix

2.86

2.13

0.93

0.79

0.75

0.75

1.30

1.09

1.09

1.80 /~-sheet

0.68

0.49

0.64

0.30

0.26

0.21

0.26

A

D

S

1.37

1.29

1.23

1.53

0.73

0.62

0.74

1.10

0.85

1.41

F

N

F

F

25 A

K

V

0.20

turn

dues 16-19. Thus the overall prediction would be a-helix for segments 1-15 and 20-26 separated by a reverse turn at positions 16-19. This gives a good correlation with the actual structure which has a-helical units over residues 1-13 and 19-27. This type of super-secondary structural unit, namely two helices orientated in an antiparallel fashion and separated by a sharp turn (Fig. 4), is a common feature in proteins.

BIOCHEMICAL EDUCATION 12(1) 1984

15

3O ¢n 2o

lO

0

10

20

length of hehcal segment

Figure 5

Histogram showing the distribution of a-helical lengths in proteins (Schulz and Schirmer, Principles of Protein Structure, page 71, ref9) ~-Sheet Protein Segments Immunoglobulins The immunoglobulins are/i-sheet rich proteins constructed from four separate chains each folded into a number of homologous domains (Fig. 6). The protein segment subjected to analysis (Table 6) is highlighted in Fig. 6. No high a-helical potential is detected in the analysis, but two units of/i-strand are clearly identified and these segments are connected by a region (7-14) of high turn potential. The high reverse-turn values are associated with the prolyprolyglycyl tripeptide, as indicated by the reverse turn positional analysis reported by Chou and Fasman.l 4 The data for proline and glycine, together with a diagrammatic representation of a reverse turn, are shown in Fig. 1. Proline displays a strong tendency to occupy positions I and 2 of a reverse turn and glycine position 3. In contrast, it is unlikely for proline to be located in a turn at positions 3 and 4. Thus the most likely position for a reverse turn can be calculated to be centred at positions 10 and 11 with units 1 - 9 and 12-22 forming the 'arms' of a/i-sheet, precisely that observed by X-ray crystallography.

Table 6

Amino Acid

D

Y

Y

The calculated structural tendencies for a known ~-sheet region of the VL immunoglobulin domain from human Bence-Jones Mcg dimer (Figure 6)

T

5 W

V

R

Q

P

10 P

G

R

G

L

15 E

W

I

G

Y

20 V

F

Y

i+5

rl i

Pa

0.40 0.37 0.650.470.30 0.17 0.180.100.11 0.290.560.970.560.72 0.51 0.380.27

p/i

1.55 3.21 2.54 1.63 0.86 0.48 0.30 0.30 0.34 0.55 0.64 0.79 1.16 1.16 1.43 2.83 3.28 2.83 /i-sheet /i-sheet

i+4

II i

i+3

1.62 0.87 0.39 0.33 0.31 0.77 3.15 5.86 5.26 4.52 1.37 0.83 0.72 0.22 0.63 0.67 0.41 0.48 0.31 Reverse Turn -~ Reverse Turn Kunitz Protease Inhibitor This type of protease inhibitor is constructed around two extended antiparallel/i-strands (Fig. 7). The analysis for this region in bovine pancreatic trypsin inhibitor is depicted in Table 7. The magnitudes of the predicted/i-sheet segments 2-11 and 18-24 are appreciably larger than the a-helical values and are thus dominant. A short unit of a-helix is predicted to occupy the intervening residues 12-17. On examination of the molecule taking into account the disulphide crosslinks it is clear that t h e / t - ~ - / i structure cannot be accommodated. Thus in view of the high/t-sheet predictions the final analysis is interpreted as antiparallel/i-sheet over residues 2 - 1 2 and 17-24, the amino acids at the individual positions 12 and 17 being included as they also show/i-sheet tendency. This final analysis gives good agreement with the X-ray structure (Fig. 7).

BIOCHEMICAL EDUCATION 12(1) 1984

16

~ L ~ I F a

-

C

b

c'~c~

s-s

'

s-s s-s

a singledo ai -- ,20 AA's

c

Lip.J

-

short chaln(L)2domalr~ long cham(H)hdomains

®

®

©

Figure 6

Diagrammatic representation o f immunoglobulin structural relationships. (a) The VL region o f human Bence-Jones Mcg dbner. The highlighted segment is herein analysed .for structural tendencies. (b} and (c} Two schematic .forms o f the whole immunogiobulin molecule where the .former clearly shows the individual structural domains o f the protein. A structural domain can be considered as a portion o f a protein which .forms a geometrically separate entity. Typically such domains contain less than 180 amino acids and correspond to a globule o.f about 25A diameter

Table 7

The calculated structural tendencies for the sequence o f amino acid residues constituting the ~sheet region o f bovine ~ancreatic trypsin inhibitor (Figure 7) 5

Amino Acid

C

K

A

1.59

1.38

0.81

0.74

1.44

0.53

K

A

1.65

1.63

1.09

0.59

0.48

0.93

0.70

R

10

I

I

R

Y

F

Y

N

0.67 a-helix

0.50

0.46

0.62

0.79

1.42

0.74

1.34

1.85

2.58

3.43

2.96

1.55 1.41 /~-sheet

0.87

0.59

0.44

0.33

0.18

0.20

0.24

0.28

0.57

0.83

0.61

0.99

0.73

15 G

L

C

Q

T

20 F

V

Y

0.90 1.46 a-helix

0.81

0.41

0.18

0.50

0.67

0.96

1.41 -:

2.38

2.74

2.08 ~-sheet

0.89

0.76

0.48

0.49

0.28

0.30

0.48

i+5

ill

t, a

i+4

I-I p/~ i

~

i+3

11 Pr i

A

The Experiment

G

G

1.33 Reverse Turn

The use of models can be a valuable aid to structural predictions and one model-building system that provides a quick and accurate test of a predicted structure is the Nicholson system,a They are, however, relatively expensive in contrast to the Ashworth-FieldhouseI s,t 6 model-building system which, although being rather flexible, is ideally suited for the construction of small peptides in undergraduate teaching laboratories,b ~ Labquip, Ashtidgewood, Forest Road, Wokingham, Near Reading, Berks, UK. Apparatus available from Coehranes of Oxford Ltd, Fairspear House, Leafield, Oxford OX8 5NT, UK. (It is reCOmmendedto purchase preformed 'Heliwire': see Biochemical Education 9, 128.)

BIOCHEMICAL EDUCATION 12(1) 1984

17

Figure 7

A diagrammatic representation of bovine pancreatic trypsin inhibitor. This example gives a clear illustration of a typical antiparallel ~-sheet which is not planar, possessing a twisting orientation within the globular protein Having followed the structural predictions outlined in this text it is recommended to give students their own sequence(s) for analysis. After making a prediction, the proposed structure should be compared with the known X-ray structure. A number of suitable sequences are presented in Table 8. An excellent source of additional data is provided in the extensive article concerning the secondary structure of proteins by Levitt and Greer. 17

Table 8

Suitable amino acid sequences for structural analysis

Source of Segrnent

Location of Segment

Reference for Determined Structure

GPVQGTIHPEAKGDTVVVTGSITGLTEGDHG

Copper zinc superoxide dismutase

12--41

18

EDGKVGTAHIIYDSVDKRLSAWSYPDADATSVSYDV

Concanavalin A

43-79

19

VLSAADKTNVKAAWSKVGGHAGEYGAEALERM FLGFPTTKTY

Horse a-haemoglobin

1-42

20

ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTP VDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNN

Bovine pancreatic phospholipase A2

1-72

21

TSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGDGIFTYDAK

Thermolysin

4-45

22

GIGAVLKVLTTGLPALISWlKRKRQQ

Melittin

entire sequence

23

GDVAKGKKTFVQKCAQCHTV

Ferricytochrome c

1-20

24

NYVSWYQQHAGKAPKVIIYEVN

Immunoglobulin (BenceJones Meg)

32-53

25

TDYTFTISSLQPEDIATYVCQQY

Immunoglobulin (BeneeJones REI)

69-91

26

QTTRENIMKLTQKIVKS

Uteroglobin

50-66

27

APLEPVYPGDNATPEQMAQYAADLRRYINMLTRPRY

Pancreatic polypeptide

entire sequence

28

Amino Acid Sequence

The beauty of such experiments is that students become familiar with the major structural architecture of globular proteins from a practical viewpoint, in contrast to the more abstract concepts generally gained from studying textbooks and lecture notes.

References

1Linderstr~m-Lang, K H and Schellman, J A (1959) The Enzymes Vol 1, 2nd ed, pp 443-510, Academic Press, New York 2Sternberg, M J E and Thornton, J M (1978) Nature 271, 15-20 3Sanger, F and Tuppy, H (1951)BiochemJ49, 463-481 Kendrew, J C, Diekerson, R E, Strandberg, B E, Hart, R G, Davies, D R, Phillips, D C and Shore, V C (1960) Nature 185,422-427; Kendrew, J C (1961) ScientAm 205, (6) 96-111

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18 s Dayhoff, M O (editor) (1972)Atlas of Protein Sequence and Structure 5 6Anf'msen, C B and Seheraga, H A (1975) Adv Prot Chem 29, 205-300 7Finney, J L, Gallatly, B J, Golton, I C and Goodfellow, J (1981)Biophys J 32, 17-33 SRiehardson, J S (1981)Adv Prot Chem 34, 167-339 9Schultz, G E and Schirmer, R H (1979) Principles of Protein Structure, pp 108-130, Springer-Verlag, New York, Heidelberg, Berlin l°schfffer, M and Edmundson, A B (1967)BiophysJ 7, 121-135 11Chou, P Y and Fasman, G D (1978) Adv Enzymology 47, 45-148 12Levitt ' M (1978) Biochemistry 17, 4277-4283 laDufton, M J and Hider, R C (1977) JMolecBiol 115,177-193 14Chou, P Y and Fasman, G D (1978) Ann Rev Biochem 47, 251-276 t SAshworth, J M and Fieldhouse, J (1971) Biochem Educ 5, 243-249 16Fieldhouse, J (1981) Biochem Educ 9, 128-132 t 7Levitt, M and Greer, J (1977)JMolecBiol 114, 181-293 1s Richardson, J S, Thomas, K A, Rubin, B H and Richardson, D C (1975)Proc Natl Acad Sci USA 72, 13491353 19Haxdma n K D and Ainsworth, C F (1972)Biochemistry 11, 4910-4919 2°Bolton, W, Cox, J M and Perutz, M F (1968)JMolec Biol 33,283-297 2t Dijkstra, B W, Kalk, K H, Hol, W G J and Drenth, J (1981)JMolecBiol 147, 97-123 22Colman, P M, Jansonius, J N and Matthews, B W (1972)JMolec Biol 70, 701-724 2STerwilliger, T C, Weissman, L and Eisenberg, D (1982)BiophysJ 37, 353-361 24Tanaka, N, Tamane, T, Tsukihura, T, Ashida, T and Kakudo, M (1975) JBiochem (Tokyo) 77, 147-162 2SEdmundson, A B, Ely, K 17,,Girling, R L, Abola, E E, Schiffer, M and Westholm, F A (1974) in Progress in Immunology II, (Brant, L and Holbrow, J, Editors) Volume 1,103-113, North-Holland, Amsterdam 26 Epp, O, Lattman, E E, S~hiffer, M, Huber, R and Palm, W (1975)Biochemistry 14, 4943-4952 27Mornon, J P, Fridlandky, F, Bally, R and Milgrom, E (1980)JMolec Biol 137,415-429 28Blundell, T L and Humbel, R E (1980)Nature 287, 781-787 International Union of Biochemistry

A d v a n c e s in M y o c a r d i o l o g y V o l u m e s 3 a n d 4

Fellowships

Edited by E Chazov, V Smirnov and N S Dhalla CVol 3), E Chazov, V Saks and G Rona (Vol 4). pp 656 and 649. Plenum Press, New York and London. 1983. $69.50 (each). ISBN 0 - 3 0 6 - 4 0 8 7 6 - 7 and ISBN 0 - 3 0 6 - 4 0 8 7 7 - 5

For Attendance at the 13th International Congress o f Biochemistry, Amsterdam, The Netherlands, August 2 5 - 3 0 , 1985 IUB and the Organizing Committee of the 13th IUB Congress will together make available awards to assist younger biochemists who wish to attend the Congress. Primary consideration will be given to residents of countries where the practice of the science of biochemistry is in the early stages of development. The Fellowships will support part of the cost of travel (normally up to a maximum of half the listed economy air fare or 70% of the APEX fare, whichever is lower) and subsistence during the Congress. The Organizing Committee of the Congress will waive the registration fee for Fellowship holders. Applications should include the following information: (1) Name and date of birth, (2) Citizenship, residence, (3) Place of work, including full postal address, (4) Nature of work, (5) List of publications, (6) Do you intend to present a contribution at the 13th IUB Congress? If so, indicate its tentative title, (7) Support available or expected to be available to the applicant, (8) Names of three referees, one of whom should, if possible, not live in the applicant's country of residence. This notice should be shown to the referees, and applicants must ask them to write to Dr Hill, at the address below, to reach him by August 15, 1984. Applications must be made in triplicate and as early as possible, arriving no later than August 15, 1984, to: Dr R L Hill, Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA. It is hoped to make known the decisions of the Selection Committee by December I, 1984. BIOCHEMICAL EDUCATION

12(1) 1984

These volumes originate in the Proceedings of 10th Congress of the International Society for Heart Research, held in Moscow in 1980. Each comprises about 60 short communications on experimental cardiology, with an occasional review article. Volume 3 covers aspects of cardiac physiology, pharmacology and biochemistry, and Volume 4, pathology (divided into hypertrophy and ischaemia). This separation is somewhat arbitrary - lipid peroxidation and cyclic nucleotide metabolism, for example, appear in both volumes. These are not books for the undergraduate, consisting mainly of detailed experimental reports, but much interesting information is present. But why is publication so long after the conference? D A Harris

M a r k e r P r o t e i n s in I n f l a m m a t i o n Edited by R C Allen, J Bienvenu, P Laurent and R M Suskind. pp 608. Walter de Gruyter, Berlin and New York. 1982. DM 185. ISBN 3 - I 1 - 0 0 8 6 2 5 - 5 The contributions to First International Symposium on Marker Proteins in Inflammation are recorded in this volume. The contributions themselves must have been very brief, as some of them run to a mere 4 pages of camera-ready copy, which is a very few words. So although the volume would give an overview of this area, I suspect it would not be of great value for preparing lectures or for the research worker. The areas covered are (1) the inflammatory response, (2) acute phase reactants, and (3) malnutrition and the immune response. A pleasant but expensive souvenir?