਀吀栀攀 一漀戀攀氀 倀爀椀稀攀 椀渀 䌀栀攀洀椀猀琀爀礀  ㄀㤀㘀㌀ 㰀⼀栀㈀㸀

਀䴀䄀堀 䘀䔀刀䐀䤀一䄀一䐀 倀䔀刀唀吀娀 ਀ 㰀椀洀最 愀氀椀最渀㴀爀椀最栀琀 戀漀爀搀攀爀㴀㈀ 猀爀挀㴀∀㄀⸀最椀昀∀㸀

The primary structure of a segment of a polypeptide chain or of a protein is the amino-acid sequence of the polypeptide chain(s), without regard to spatial arrangement (apart from configuration at the alpha-carbon atom). This definition does not include the positions of disulphide bonds, and is, therefore, not identical with "covalent structure" (IUPAC-IUB, 1970). The commonly occurring amino acids are of 20 different kinds which contain the same dipolar ion group H3N+.CH.COO-. They all have in common a central carbon atom to which are attached a hydrogen atom, an amino group (NH2) and a carboxyl group (COOH). The central carbon atom is called the Calpha-atom and is a chiral centre. All amino acids found in proteins encoded by the genome have the L-configuration at this chiral centre.਀㰀⼀瀀㸀㰀瀀㸀 ਀ This configuration can be remembered as the CORN law. Imagine looking along the H-Calpha bond with the H atom closest to you.਀㰀椀洀最 愀氀椀最渀㴀挀攀渀琀攀爀 猀爀挀㴀∀㌀⸀最椀昀∀㸀 When read clockwise, the groups attached to the Calpha spell the word CORN (Richardson, 1981). There are 20 side chains found in proteins encoded by the genetic machinery of the cell. The side chains confer important properties on a protein such as the ability to bind ligands and catalyse biochemical reactions. They also direct the folding of the nascent polypeptide and stabilise its final conformation. In molecular graphics, atoms can be represented in different ways. For expedience, molecules are often displayed only as lines or vectors between the atoms bonded together covalently. An elegant representation is the ball-and-stick type in which atoms are drawn as coloured spheres and their bonds as rod-like connections. Another useful display is the space-filling representation in which a surface is drawn around the atoms to indicate their van der Waals radii. This surface can be drawn as a series of dots or as a solid entity (Lesk, 1991). Amino acids in proteins(or polypeptides) are joined together by peptide bonds. The sequence of R-groups along the chain is called the primary structure.਀ ਀㰀⼀瀀㸀㰀瀀㸀 The Peptide bond

਀ Pauling et al. (1951) analysed the geometry and dimensions of the peptide bonds in the crystal structures of molecules containing either one or a few peptide bonds. Their results are summarised in the diagram below where the consensus bond lengths are shown in Angstrom units. Bond angles in degrees are also shown for the peptide N and C atoms. It should be noted that the C-N bond length of the peptide is 10% shorter than that found in usual C-N amine bonds (Schulz and Schirmer, 1990; Creighton, 1993). ਀㰀⼀瀀㸀㰀瀀㸀 ਀ This is because the peptide bond has some double bond character (40%) due to resonance which occurs with amides. The two canonical structures are: ਀㰀⼀瀀㸀㰀瀀㸀 ਀ As a consequence of this resonance all peptide bonds in protein structures are found to be almost planar, i.e. atoms Calpha(i), C(i), O(i), N(i+1) and Calpha(i+1) are approximately co-planar. This rigidity of the peptide bond reduces the degrees of freedom of the polypeptide during folding. The peptide bond nearly always has the trans configuration since it is more favourable than cis, which is sometimes found to occur with proline (Pro) residues (Schulz and Schirmer, 1990). ਀

਀ As can be seen from the previous page, steric hindrance between the functional groups attached to the Calpha atoms will be greater in the cis configuration. However, for proline residues, the cyclic nature of the side chain means that both cis and trans configurations have more equivalent energies. Thus proline is found in the cis configuration more frequently than the other amino acids.਀㰀⼀瀀㸀㰀瀀㸀 Properties of amino acids

਀ The sequence and properties of side chains determine all that is unique about a particular protein, including its biological function and its specific three-dimensional structure. ਀ Histidine (His) is the only side chain that titrates near physiological pH, making it especially useful for enzymatic reactions. ਀㰀⼀瀀㸀㰀瀀㸀 ਀ Lysine (Lys) and arginine (Arg) are normally positively charged and aspartate (Asp) and glutamate (Glu) are negatively charged. These charges are very seldom buried in protein interiors except when they are serving some special purpose, as in the activity and activation of chymotrypsin (Blow et al., 1969; Wright, 1973). ਀㰀⼀瀀㸀㰀瀀㸀 ਀ Asparagine (Asn) and glutamine (Gln) have interesting hydrogen-bonding properties, since they resemble the backbone peptides. The hydrophobic residues provide a very strong driving force for folding, through the indirect effect of their ceasing to disrupt the water structure once they are buried (Kauzmann, 1959). They also, however, affect the structure in a highly specific manner because their varied sizes and shapes fit together in very efficient packing (Lee and Richards, 1971). ਀

਀ Proline has stronger stereochemical constraints than any other residue, with only one instead of two variable backbone angles, and it lacks the normal backbone NH for hydrogen bonding. It is both disruptive to regular secondary structure and also good at forming turns in the polypeptide chain, so that in spite of its hydrophobicity it is usually found at the edge of the protein (Richardson, 1981). ਀

਀ Glycine (Gly) has three different unique capabilities. As the smallest side group (only a hydrogen), it is often found where main chains approach each other very closely. In addition Gly can assume conformations normally restricted by close contacts of the beta-carbon and finally it is more flexible than other residues, thus contributing to parts of the backbone that need to move or hinge (Richardson, 1981). ਀㰀⼀瀀㸀㰀瀀㸀 ਀ Serine (Ser) and threonine (Thr) carry aliphatic hydroxyl groups capable of forming hydrogen bonds with suitable donor or acceptor groups, such as the imino nitrogen or the carbonyl oxygen of the main polypeptide chain. Serine reacts with phosphate by an ester bond, forms part of the catalytic site of many hydrolytic enzymes (Dickerson and Geis, 1969) and contributes to the lining of ion channels. Serine, threonine, and asparagine are also the binding sites of carbohydrates that are attached to the surface of many proteins. Carbohydrates bound to serine and threonine form O-glycosidic bonds and those linked to asparagine form N-glycosidic bonds (Perutz, 1992). ਀

਀ Cysteine (Cys) carries the highly reactive sulphydryl group. This does not ionise at physiological pH nor form hydrogen bonds of significant strength, but two cysteines placed some distance apart along a polypeptide chain, or forming part of different chains, can be joined by oxidation to form the disulphide bridge of cystine which plays an important part in stabilizing protein structures. Disulphide bonds increase the conformational stability mainly by constraining the unfolded conformations of the protein and thereby decreasing their conformational entropy (Pace, 1990). Cysteines also bind zinc, copper, and iron ions. The sulphur atom in methionine is unreactive and generally serves no function other than imposing a special configuration on the aliphatic sidechain, but in cytochrome c it forms the link between the protein and the heme iron (Olson, 1992). ਀

਀ ਀ ਀倀爀漀琀攀椀渀 猀琀爀甀挀琀甀爀攀 搀攀琀攀爀洀椀渀愀琀椀漀渀 㰀⼀瀀㸀㰀瀀㸀 ਀䤀渀 琀攀爀洀猀 漀昀 琀栀攀 愀挀挀甀爀愀挀礀 漀昀 瀀爀漀琀攀椀渀 猀琀爀甀挀琀甀爀攀 搀攀琀攀爀洀椀渀愀琀椀漀渀猀Ⰰ 愀氀氀 漀昀 琀栀攀 戀漀渀搀 氀攀渀最琀栀猀 愀爀攀 椀渀瘀愀爀椀愀渀琀⸀ 䈀漀渀搀 愀渀最氀攀猀 愀爀攀 愀氀猀漀 攀猀猀攀渀琀椀愀氀氀礀 椀渀瘀愀爀椀愀渀琀Ⰰ 攀砀挀攀瀀琀 瀀攀爀栀愀瀀猀 昀漀爀 Ⰰ 琀栀攀 戀愀挀欀戀漀渀攀 一ⴀ䌀愀氀瀀栀愀ⴀ䌀 愀渀最氀攀⸀ 吀栀攀 愀氀瀀栀愀ⴀ挀愀爀戀漀渀 椀猀 琀攀琀爀愀栀攀搀爀愀氀Ⰰ 眀栀椀挀栀 眀漀甀氀搀 最椀瘀攀 ㄀㄀　뀀Ⰰ 戀甀琀 琀栀攀爀攀 愀爀攀 椀渀搀椀挀愀琀椀漀渀猀 昀爀漀洀 愀挀挀甀爀愀琀攀氀礀 爀攀昀椀渀攀搀 瀀爀漀琀攀椀渀 猀琀爀甀挀琀甀爀攀猀 ⠀䐀攀椀猀攀渀栀漀昀攀爀 愀渀搀 匀琀攀椀最攀洀愀渀渀Ⰰ ㄀㤀㜀㔀㬀 圀愀琀攀渀瀀愀甀最栀 攀琀 愀氀⸀Ⰰ ㄀㤀㜀㤀⤀ 琀栀愀琀  挀愀渀 猀漀洀攀琀椀洀攀猀 猀琀爀攀琀挀栀 琀漀 氀愀爀最攀爀 瘀愀氀甀攀猀 椀渀 漀爀搀攀爀 琀漀 愀挀挀漀洀洀漀搀愀琀攀 漀琀栀攀爀 猀琀爀愀椀渀猀 椀渀 琀栀攀 猀琀爀甀挀琀甀爀攀⸀ 吀栀攀 搀椀栀攀搀爀愀氀 愀渀最氀攀  愀琀 琀栀攀 瀀攀瀀琀椀搀攀 椀猀 瘀攀爀礀 挀氀漀猀攀 琀漀 ㄀㠀　뀀 ⠀瀀爀漀搀甀挀椀渀最 愀 琀爀愀渀猀Ⰰ 瀀氀愀渀愀爀 瀀攀瀀琀椀搀攀 眀椀琀栀 琀栀攀 渀攀椀最栀戀漀甀爀椀渀最 愀氀瀀栀愀ⴀ挀愀爀戀漀渀猀 愀渀搀 琀栀攀 一Ⰰ 䠀Ⰰ 䌀Ⰰ 愀渀搀 伀 戀攀琀眀攀攀渀 琀栀攀洀 愀氀氀 氀礀椀渀最 椀渀 漀渀攀 瀀氀愀渀攀⤀⸀ 吀栀攀 爀攀洀愀椀渀椀渀最 搀椀栀攀搀爀愀氀 愀渀最氀攀猀 愀爀攀 琀栀攀 猀漀甀爀挀攀 漀昀 攀猀猀攀渀琀椀愀氀氀礀 愀氀氀 琀栀攀 椀渀琀攀爀攀猀琀椀渀最 瘀愀爀椀愀戀椀氀椀琀礀 椀渀 瀀爀漀琀攀椀渀 挀漀渀昀漀爀洀愀琀椀漀渀⸀ 吀栀攀 戀愀挀欀戀漀渀攀 搀椀栀攀搀爀愀氀 愀渀最氀攀猀 愀爀攀  愀渀搀  椀渀 猀攀焀甀攀渀挀攀 漀爀搀攀爀 漀渀 攀椀琀栀攀爀 猀椀搀攀 漀昀 琀栀攀 愀氀瀀栀愀ⴀ挀愀爀戀漀渀Ⰰ 猀漀 琀栀愀琀  椀猀 琀栀攀 搀椀栀攀搀爀愀氀 愀渀最氀攀 愀爀漀甀渀搀 琀栀攀 一ⴀ䌀愀氀瀀栀愀 戀漀渀搀 愀渀搀  愀爀漀甀渀搀 琀栀攀 䌀愀氀瀀栀愀ⴀ䌀 戀漀渀搀⸀ 吀栀攀 猀椀搀攀 挀栀愀椀渀 搀椀栀攀搀爀愀氀 愀渀最氀攀猀 愀爀攀 ㄀Ⰰ ㈀Ⰰ 攀琀挀⸀ 䄀渀 攀砀琀爀攀洀攀氀礀 甀猀攀昀甀氀 搀攀瘀椀挀攀 昀漀爀 猀琀甀搀礀椀渀最 瀀爀漀琀攀椀渀 挀漀渀昀漀爀洀愀琀椀漀渀 椀猀 琀栀攀 刀愀洀愀挀栀愀渀搀爀愀渀 瀀氀漀琀 ⠀刀愀洀愀挀栀愀渀搀爀愀渀 攀琀 愀氀⸀Ⰰ ㄀㤀㘀㌀⤀ 眀栀椀挀栀 瀀氀漀琀猀  愀渀搀 ⸀ 吀栀攀 瘀愀氀甀攀猀 漀昀  愀渀搀  琀栀愀琀 愀爀攀 瀀漀猀猀椀戀氀攀 愀爀攀 挀漀渀猀琀爀愀椀渀攀搀 最攀漀洀攀琀爀椀挀愀氀氀礀 搀甀攀 琀漀 猀琀攀爀椀挀 挀氀愀猀栀攀猀 戀攀琀眀攀攀渀 渀漀渀ⴀ渀攀椀最栀戀漀爀椀渀最 愀琀漀洀猀⸀ 吀栀攀 瀀攀爀洀椀琀琀攀搀 瘀愀氀甀攀猀 漀昀  愀渀搀  愀爀攀 椀渀搀椀挀愀琀攀搀 漀渀 愀 琀眀漀ⴀ搀椀洀攀渀猀椀漀渀愀氀 洀愀瀀 漀昀 琀栀攀  ⴀ  瀀氀愀渀攀 ⠀䈀爀愀渀搀攀渀 愀渀搀 吀漀漀稀攀Ⰰ ㄀㤀㤀㄀⤀⸀  ਀ 㰀⼀瀀㸀㰀瀀㸀 ਀ ਀ Secondary Structure

਀ The secondary structure of a segment of polypeptide chain is the local spatial arrangement of its main-chain atoms without regard to the conformation of its side chains or to its relationship with other segments (IUPAC-IUB, 1970). There are three common secondary structures in proteins, namely alpha helices, beta sheets and turns. That which cannot be classified as one of the standard three classes is usually grouped into a category called "other" or "random coil". This last designation is unfortunate as no portion of protein three dimensional structure is truly random and it is not a coil either. Regular secondary structure conformations in segments of a polypeptide chain occur when all the bond angles in that polypeptide segment are equal to each other, and all the bond angles are equal. The rotational angles for and bonds for common regular secondary structures are shown in the table below.਀

਀ Max Ferdinand Perutz was born in Vienna on May 19th, 1914. Both his parents, Hugo Perutz and Dely Goldschmidt, came from families of textile manufacturers who had made their fortune in the 19th century by the introduction of mechanical spinning and weaving into the Austrian monarchy. He was sent to school at the Theresianum, a grammar school derived from an officers academy of the days of the empress Maria Theresia, and his parents suggested that he should study law in preparation for entering the family business. However, a good schoolmaster awakened his interest in chemistry, and he had no difficulty in persuading his parents to let him study the subject of his choice.਀㰀⼀瀀㸀㰀瀀㸀 In 1932, he entered Vienna University, where he, in his own words, "wasted five semesters in an exacting course of inorganic analysis". His curiosity was aroused, however, by organic chemistry, and especially by a course of organic biochemistry, given by F. von Wessely, in which Sir F.G. Hopkins' work at Cambridge was mentioned. It was here that Perutz decided that Cambridge was the place where he wanted to work for his Ph.D. thesis. With financial help from his father he became a research student at the Cavendish Laboratory in Cambridge under J.D. Bernal in September 1936, and he has stayed at Cambridge ever since.਀㰀⼀瀀㸀㰀瀀㸀 After Hitler's invasion in Austria and Czechoslovakia, the family business was expropriated, his parents became refugees, and his own funds were soon exhausted. He was saved by being appointed research assistant to Sir Lawrence Bragg, under a grant from the Rockefeller Foundation, on January 1st, 1939. The grant continued, with various interruptions due to the war, until 1945, when Perutz was given an Imperial Chemical Industries Research Fellowship. In October 1947, he was made head of the newly constituted Medical Research Council Unit for Molecular Biology, with J.C. Kendrew representing its entire staff. He continued holding this post until he was made Chairman of the Medical Research Council Laboratory of Molecular Biology, in March 1962. His collaboration with Sir Lawrence Bragg has continued through all these years.਀㰀⼀瀀㸀㰀瀀㸀 The scientific work of Perutz on the structure of haemoglobin started as a result of a conversation with F. Haurowitz in Prague, in September 1937. G.S. Adair made him the first crystals of horse haemoglobin, and Bernal and I. Fankuchen showed him how to take X-ray pictures and how to interpret them. Early in 1938, Bernal, Fankuchen, and Perutz [Nature, 141 (1938) 523] published a joint paper on X-ray diffraction from crystals of haemoglobin and chymotrypsin. The chymotrypsin crystals were twinned and therefore difficult to work with, and so Perutz continued with haemoglobin. D. Keilin, then Professor of Biology and Parasitology at Cambridge, soon became interested in the work and provided Perutz and his colleagues with the biochemical laboratory facilities which they lacked at the Cavendish. Thus from 1938 until the early fifties the protein chemistry was done at Keilin's Molteno Institute and the X-ray work at the Cavendish, with Perutz busily bridging the gap between biology and physics on his bicycle. The rest of the story is well-known and forms the subject of his Nobel discourse.਀㰀⼀瀀㸀㰀瀀㸀 Perutz has persued one sideline concerned with glaciers, studying their crystal texture and mechanism of flow, but this was mainly an excuse for working in the mountains: he is a keen mountaineer, his other recreations being walking, skiing and gardening. Scientifically, his overwhelming interest lies on the side of molecular biology. He is grateful for having had the good fortune of being joined by colleagues of great ability, several of whom have now been honoured with the Nobel Prize at the same time as Perutz himself. Kendrew came in 1946, Crick in 1948, and Watson arrived as a visitor in 1951. Recently F. Sanger, who received the Nobel Prize in 1958, also joined forces with them. Perutz is extremely happy at the generous recognition given by the Swedish Academy of Sciences and the Royal Karolinska Institute to their great common adventures and hopes that it will spur them to new endeavours.਀㰀⼀瀀㸀㰀瀀㸀 Perutz, who is a Fellow of the Royal Society, was made Companion of the British Empire in 1962. He is also an honorary member of the American Academy of Arts and Sciences.਀㰀⼀瀀㸀㰀瀀㸀 In 1942, Perutz married Gisela Peiser. They have two children, Vivien (b. 1944) and Robin (b. 1949).਀㰀⼀瀀㸀㰀瀀㸀 ਀ ਀ ਀ ਀ ਀ ਀ ਀ ਀ ਀