Structural Bioinformatics (C3210) Protein Structure

Transcription

1 Structural Bioinformatics (C3210) Protein Structure

2 Great Diversity of Protein Biological Functions The primary responsibility of proteins is to execute the tasks directed by genomic information. The proteins display high diversity and a wide variety of specialized functions: enzymes catalyze all vital chemical reaction of the cell. Each enzyme catalyzes one particular reaction of covalent bond breakage or formation signaling proteins such as hormones and neurotransmitters transmit information between specific cells and organs receptor proteins used by cells to detect chemical and physical signals and transmit them to the cell's response machinery transport and storage proteins carry and store a variety of particles ranging from macromolecules to electrons structural proteins provide mechanical support to cells and tissues defense proteins participate in the immune systems of complex organisms to defend against intruders (the best known are antibodies) gene regulatory proteins bind to the DNA and control gene expression by switching genes on and off 2

3 Amino acids: Building Blocks of Proteins Amino Acids are the building blocks of proteins. All proteins are linear polymers made up of various combinations of 20 amino acids, and are composed mainly of C, H, O, N and S atoms. The amino acid sequence that defines the protein is determined by the genetic code. 3

4 α-amino Acids The amino acids found in proteins have the following general topology: An α-amino acid is characterized by a central carbon atom (called the Cα), which is connected to the following four groups: (1) amino; (2) carboxyl; (3) hydrogen atom and (4) distinctive R group - often referred to as the side chain. 4

5 α-amino Acid Stereoisomers With four different groups connected to the central sp3 carbon α, α-amino acids are chiral and possess two stereoisomers: the L and the D enantiomers. The amino acids in nearly all natural proteins have the L stereochemistry. 5

6 Standard 20 Amino Acids 6

7 Diversity of the Properties of Amino Acids Each of the twenty amino acids has unique physico-chemical properties depending on the nature of its side chain (R group). The amino acid side chains vary in size, shape, charge, hydrogen bonding capacity, hydrophobic character and chemical reactivity. 7

8 Classification of Amino Acids Properties The amino acids can be classified and organized in different groups, based on their various physico-chemical properties as indicated in the following diagram. Small Hydrophobic Amphipathic Pro Gly Ala Aliphatic Leu Val Ile Thr Met Phe Aromatic Ser Cys Tiny Asn Asp Gln Polar Glu Trp Tyr Negative Arg His Lys Charged Positive 8

9 Amino Acid Hydrophobicity and Hydrophility 9

10 Non-Standard Amino Acids In addition to the standard set of twenty amino acids that are found in all proteins, other amino acids have been found in certain types of proteins. Selenocysteine and pyrrolysine were found in some methanogenic archaea (they are genetically encoded in DNA in the same way as 20 standard amino acids). Others are the result of biochemical transformations of a standard amino acid, after its incorporation into the protein sequence. Pyrrolysine 10

11 From Amino Acids to Proteins 11

12 Amino Acids are Linked by Peptide Bonds Amino acids can be covalently linked together by the formation of an amide bond between the α-amino group of one amino acid and the α-carboxyl group of another amino acid. The resulting amide bond is known as peptide bond. The formation of a dipeptide from two amino acids in a condensation reaction is accompanied by the removal of a water molecule. 12

13 Peptide Biosynthesis In the cell, amino acids are chemically linked by the biochemical process of translation (protein biosynthesis). In translation, messenger RNA (produced by transcription) is processed by ribosome to produce amino acid chain, that will later fold into an active protein. Video:

14 Polymer Amino-Acids A series of amino acids joined by peptide bonds form a polypeptide chain. Each amino acid unit is called a residue. A polypeptide chain consists of a regularly repeating part, called the main chain or the backbone and a variable part, comprising the distinctive side chains. 15

15 Length of Proteins Natural proteins contain between 50 and 2000 amino acid residues. Shorter chains are called oligopeptides or simply peptides. The following histogram shows the length of the proteins in the E. coli proteome. 16

16 More than One Polypeptide Chain Some proteins contain a single polypeptide chain, whereas others may aggregate to form dimeric, trimeric and multimeric clusters. The polypeptide chains in these clusters can be either identical or different. 17

17 Conjugated Proteins There are proteins that incorporate non-peptidic molecules in their overall structure, either bonded covalently or positioned by other forces. These are called conjugated proteins, and the nonpeptide components are referred to as prosthetic groups. The prosthetic moieties play an essential role in protein function. Conjugated proteins are classified according to the chemical nature of their prosthetic group. 18

18 Cross-Linked Polypeptide Chains In some proteins, two cysteine side chains are located close together so that their thiol groups can be oxidized to produce a covalently dimeric amino acid joined by a disulfide bond (bridge). This dimeric amino acid is known as cystine. The covalent crosslinking helps to stabilize the protein structure. Intramolecular disulfide bonds are mainly found in proteins that are in the extracellular space (e.g. digestive enzymes, hormones). 19

19 Geometry of Proteins and Peptides 20

20 Peptide Bonds are Planar The peptide bond is essentially planar. All the atoms in the central amide bond lie in the same plane. 21

21 Peptide Bond is Planar The chemical nature of the peptide bond explains its planarity. The lone pair on the nitrogen atom can delocalize into the adjacent carbonyl as illustrated in the following resonance structure. Thus, the peptide bond has a considerable double-bond character, which prevents free rotation about this bond and favors a planar geometry. 22

22 Cis and Trans Isomers of the Peptide Bond The restricted rotation about the planar peptide bond allows the amide moieties to exist as discrete s-cis and s-trans isomers. In proteins, the great majority of peptide bonds are s-trans. 23

23 Trans Isomer Favored The preference of the s-trans over the s-cis isomer can be explained by steric clashes between the amino acids side chains attached to the α-carbon which hinder formation of the s-cis isomer. 24

24 Isomers of Proline For proline the situation is different because the steric differences between cis and trans isomers are minimal. In folded proteins about 10% of the proline-peptide bonds are found in the cis conformation, which is significantly more than for other amino acids. 25

25 Peptide Torsion Angles The torsion angles along the polypeptide chain are called omega (ω) (the peptide bond), phi (φ) and psi (ψ). Unlike the peptide bond, the bonds defined by the torsion angles φ and ψ are single σ-bonds and can rotate. 26

26 Conformational Freedom The free rotation about two rotatable bonds of each amino acid allows adjacent rigid peptide units to rotate about these bonds, and as a consequence the polypeptide chain can fold in many different ways. The exact geometry of a polypeptide chain is defined by the respective φ and ψ values. 27

27 Conformational Complexity of Polypeptide Chains With two rotatable bonds for each amino acid, the conformational complexity of any polypeptide chain is huge. Just taking the three energetically favoured staggered conformation for each rotatable bond yields the following results: 28

28 Not All φ/ψ Torsion Angles are Possible Whereas there is considerable conformational freedom around the φ and ψ angles, not all torsion angles are possible due to steric repulsions. For example, in the situation illustrated below the combination of ψn-1=180 and φn=0 is "disallowed" due to steric clashes between the two carbonyl groups. 29

29 The Ramachandran Plot G.N. Ramachandran used computer models of various dipeptides to systematically explore possible φ and ψ combinations in polypeptide chains. Each combination of the two torsion angles was structurally examined to identify favorable interactions or steric clashes between atoms. The distribution of φ and ψ angles can be plotted in two-dimensions in the so-called Ramachandran plot (see next pages). 30

30 φ and ψ Distribution For all amino acids except glycine, the following Ramachandran plot describes the allowed and disallowed φ-ψ torsion angle combinations. The white areas correspond to disallowed conformations (where atoms clash). The blue areas correspond to allowed conformations. Borderline regions in which the atoms are allowed to come a little bit closer together appear in light blue. 31

31 Torsion Angles Observed in Proteins By displaying all sets of φ/ψ torsion angles observed in a given protein (here, the lysozyme protein) on top of a Ramachandran plot, the fit between the predicted and observed values can be checked (glycine residues are not included in this diagram). 32

32 Glycine Residue Torsion Angles In the case of glycine the situation is different because this residue has no side chain, which allows for a broader range of φ/ψ values. Glycine residues are often located in areas of Ramachandran plot that are disallowed for other amino acids. 33

33 Side Chain Conformations For similar reasons as for the geometry of the backbone the conformational possibilities of the side chains are also restricted. Low energy conformations of a given residue are called side chain rotamers. The side chain dihedral angles are called by letter χ of the Greek alphabet and number (χ1, χ2, χ3, χ4, χ5). In principle, the torsion angles adopted by side chain residues should be close to theoretical equilibrium values, which minimize close contacts between adjacent atoms of the residue (e.g. staggered in the case of a sp3-sp3 bond and eclipsed for a sp2sp3 bond). However, some combinations of torsion angles can create unfavourable interactions between distant atoms. 34

34 Non-Rotameric Side Chain Conformations The side chain conformations are highly affected by external parameters, such as ligand binding and protein-protein interactions. Consequently, commonly up to 10% of the side chains in a protein adopt non-regular (non-rotameric) conformations. For example, in the following enzyme nonrotameric side chains are shown with green carbon atoms. Note that three of these residues were found to interact with the ligand molecule (white) in the complex. 35

35 Protein Structure Overview 36

36 Forces Involved in Protein Stability Protein stability arises from many noncovalent interactions such as hydrogen-bonding, hydrophobic and electrostatic interactions. Their individual forces are weak (many hundred times weaker than the strength of a covalent bond), but their great number and broad distribution create a cooperative effect that dictates how the protein fold into a conformation. 37

37 Representing Protein Structures Various representations are used to visualize protein structures, each type highlighting a specific feature of the considered structure. The most common visualization techniques are illustrated here using the thioredoxin protein as an example. Wireframe Ribbon Ball & Stick CPK Cartoon Cα trace Surface 38

38 The Four Levels of Protein Architecture There are four levels in the hierarchy of the protein structure: primary structure is defined by the amino acid sequence secondary structure includes local regular conformations of the polypeptide chain. The two major elements of the secondary structure are the α-helix and the β-sheet tertiary structure of a protein is the overall 3D architecture of the folded polypeptide chain which also includes the assembly of the various secondary structure elements in 3D proteins consisting of more than one polypeptide chain display a quaternary structure, which refers to the spatial relationship between the individual polypeptide chains (subunits) 39

39 Primary Structure The primary structure of a protein accounts for its covalent structure. Thus, the primary structure is a linear description of the sequence of amino acids of the protein (and may include posttranslational modifications, such as glycosylation, phosphorylation and the locations of disulfide bonds). 40

40 Unique Primary Structure for Each Protein In 1953 Frederick Sanger determined the first amino acid sequence of a protein (it was for the hormone insulin). He showed that proteins have a unique amino acid sequence. All molecules of a given protein are identical, and the sequence of a protein is unique. 41

41 Secondary Structure The secondary structure refers to recurring local conformations of the polypeptide chain backbone. The two major elements of the secondary structure are the α-helix and the β-sheet. Subsequently, other local non-periodic structural elements, such as turns and specific loops were identified. All the secondary structure elements are folded by linking the C=O and N-H groups of the backbone together by means of hydrogen bonds. 42

42 The α-helix The α-helix is the best known and most abundant form of local regular structures found in proteins. In this structure the C=O and N-H groups of all the peptide units are hydrogen-bonded. The C=O hydrogen bond acceptors and their corresponding N-H donor groups are separated by four amino acids (i.e. Oi and Ni+4) in the polypeptide chain. 43

43 Packing of the α-helix The α-helix includes the tight pack of backbone atoms. The side chains (represented here by green spheres in the Cβ position) extend outwards, also in a helical array. 44

44 φ and ψ Torsion Angles of the α-helix The α-helix can be defined by its φ and ψ torsion angles. When all of the residues of a polypeptide stretch have φ and ψ angles of approximately -57 and -47 respectively, these residues form an α-helix. 45

45 Two Enantiomeric α-helices In fact two α-helix structures can be defined: the right-handed (clockwise) and left-handed (counterclockwise) helices (with φ/ψ values of -57 /-47 and +57 /+47, respectively). The righthanded α helix is by far the most abundant form found in proteins. 46

46 Geometry Described with Pitch and Rise The helical structure repeats itself every 360, in which the distance translated along the helical axis is 5.4 Å, which is the pitch of the helix. α-helices have 3.6 amino acid residues per turn. 47

47 Helix Macro-Dipole α-helix has an overall dipole moment caused by the aggregate effect of all the individual dipoles from the carbonyl groups of the peptide bond pointing along the helix axis. The cumulative effect results in a substantial macro-dipole for the helix, with a positive value at the amino end (N-terminal), and a negative charge at the carboxyl end (C-terminal). The N-terminal often binds negatively charged ligands. 48

48 Amphipathic Character of the α Helix Many α-helices are amphipathic, i.e. they consist of hydrophobic non-polar side chains along one side of the helical cylinder, and hydrophilic polar residues along the other side. These helices often aggregate with other hydrophobic surfaces. The amphipathic nature of a helix is best seen by use of a helical wheel, which is a projection of the helix looking down at the main axis. 49

49 310-Helix and π-helix There are at least three well-identified regular helices types in proteins. All the helices visualized here consist of a string of 16 amino acids colored according to the atom types with the side chains represented as green spheres. The following view shows the ideal right-handed α-helix, the more stretched 310-helix, and the more compact π-helix. 50

50 Helices Geometrical Parameters The parameters of the three types of helices presented in the previous page are summarized here. 51

51 Occurrence of Helices in Proteins The α-helix is found in many proteins. The 310-helix structure is much less widespread and may be found at the beginning or at the end of an α-helix (in a stretch of up to 4 residues). The π-helix appears to be extremely rare and is considered to be unstable. 52

52 The β-sheet The β-pleated sheet or simply "β-sheet" is another major structural element in proteins. As in the α-helix, the structural elements of the β-sheet are held together by hydrogen bonds between N-H and C=O groups of peptide units. 53

53 The β-strand Unit The basic unit of the β-sheet is a single polypeptide chain with an extended, zigzag like conformation, called the β-strand. The side chains (green spheres) of neighboring residues in the β-strand point in opposite directions. 54

54 φ and ψ Torsion Angles in β-sheets A relatively broad range of extended structures is sterically possible. Typical values are ψ=140 and φ=

55 Parallel and Anti-Parallel β-sheets The β-strand are much more stable when two or more strands are associated by main chain hydrogen bond interactions, and form a sheet. Adjacent strands in a β-sheet can be either parallel (same direction of the polypeptide chain) or anti-parallel (opposite direction of the polypeptide chain). The hydrogen bonding pattern in the two sheets is somewhat different. 56

56 Occurrence of β-sheets in Proteins There is no special preference observed for parallel or antiparallel β-sheet formation. In a protein, one can find pure parallel or anti-parallel β-sheets, and also a combination of both types. 57

57 Twist of the β-sheet The β-sheet model theoretically presented was planar; however most β-sheets observed in proteins are twisted with a twist that is always left-handed (as indicated below). The twist of the sheet results from a torsion in the strand of about 0-30 per residue. 58

58 Turns Another important type of secondary elements is the turn, which is used to reverse the direction of the polypeptide chain. Various types of turns are found in proteins, which differ in the number of residues, the backbone torsion angles, and the hydrogen bond pattern. Here are some examples: 59

59 β-turns Type I and Type II β-turns are frequently found in protein structures. In these turn types a hydrogen bond is formed between the backbone C=O group and N-H group separated by two residues (i.e. hydrogen bond between residue i and residue i+3 of the turn). Different β-turns have different conformations. The torsion angles for residues i+1 and i+2 in type I and type II β-turns are indicated in the following Ramachandran plot. Note that in a type II β-turn, residue i+2 lies in a region that was allowed only for glycine dipeptides. 60

60 Non-Regular Coil and Loops Approximately 80-90% of the residues in proteins can be classified as participating in secondary structures (α-helix, βsheet or turn). All other residues possess non-regular structures that are described as coils or loops. 61

61 Loops A loop is any stretch of a non-regular polypeptide chain connecting secondary structures. Among the many possible loop conformations, several specific structures have been identified and added to the repertoire of secondary structures. One type of loop-like chain is the Ω-loop in which the beginning and end of the loop are very close together (visualized below in white color). 62

62 Coil A "coil" is the terminology which is used to describe the structure of a polypeptide chain that does not fall into the categories of helix, sheet or turn. 63

63 Super-Secondary Structures and Motifs Secondary structural elements can be combined to define precise three-dimensional architectures. In many cases it is possible to identify recurring patterns of secondary structure organization in many different proteins, even with completely different sequences. These patterns are called super-secondary structures or structural motifs. 64

64 Classification of Super-Secondary Structures There are three main classes of super-secondary structures: all-α, all-β and mixed α/β structures. Simple super-secondary structures consist of 2 to 3 secondary elements. These can be assembled into larger super-secondary structures that are sometimes referred as folds. 65

65 All β super-secondary structures Representative β-super-secondary structures are illustrated in the following pages. The super-secondary structures are represented by both their 3D architecture and by their 2D schematic topological arrangement. 66

66 β-hairpin The "β-hairpin" is one of the simplest and most common supersecondary structures. It includes two consecutive anti-parallel βstrands connected by short loop of two to five amino acids. The loop itself is referred to as the β-hairpin loop. Beta hairpins can occur in isolation or as part of a series of hydrogen bonded strands that collectively comprise a beta sheet. 67

67 β-meander β-hairpins can be combined into consecutive anti-parallel βstrands and form the "β-meander" super-secondary structure. 68

68 Greek-Key Another combination of β-strands is the Greek-key supersecondary structure. This is a four-stranded β-sheet motif which is characterized by the topology indicated below. In 3D, this motif can adopt a variety of architectures, either with all four strands in the same β-sheet or in two different sheets, as seen here. 69

69 All α Super-Secondary Structures Representative α-super-secondary structures are illustrated in the following pages. The super-secondary structures are described by both their 2D schematic topological arrangement and their 3D architecture. 70

70 αα-hairpin Helix hairpin or αα-hairpin loops connect two sequential α-helices which lie adjacent in space and run approximately anti-parallel. Note the tight packing between the two helices, which is usually achieved by hydrophobic interactions between the side chains. 71

71 αα-corners αα-corners are short loops which connect helices that are roughly perpendicular. The motif is highly common, although it may serve different roles in different proteins. 72

72 EF Hand Some super-secondary structures have important functions, for example the EF hand, which is used for calcium binding. This is a view of a helix-loop-helix in which the two helices are roughly perpendicular. The loop is made up of about 12 residues with a conserved sequence. 73

73 Helix-Turn-Helix Another important functional helix-loop-helix super secondary structure is called the helix-turn-helix (HTH), although it does not include a true reverse turn geometry. This super secondary structure is used for DNA binding. The HTH is generally composed of two α-helices connected by a short loop of usually 4 conserved residues. The helices are oriented at about 120. One helix (the yellow helix in the view) is the DNA recognition helix which lies in the DNA major groove. This motif is found in many proteins that regulate gene expression. 74

74 Four-Helix Bundle The "Four-Helix Bundle", in which 4 α-helices are packed together, is another type of common super-secondary structure. This motif has several topologies, as can be seen here. Typically the tight packing of the helices is a result of the amphipathic nature of the helices that puts hydrophobic residues in the interface between the helices and the polar side chains on the outside surface. 75

75 Mixed α & β Super-Secondary Structures Representative α/β-super-secondary structures are described in the following pages. The super-secondary structures are represented by both their 2D schematic topological arrangement and their 3D architecture. 76

76 β-α-β Motif The "β-α-β" super-secondary structure consists of a β-strand-loopα-helix-loop-β-strand. This motif connects two parallel strands and is found in proteins that have parallel β-sheets. The three secondary structure elements are tightly packed and create a hydrophobic core. The loop regions in the motif can vary in length from one residue to more than 100 residues. 77

77 Rossmann Fold An extension of the β-α-β super-secondary structure can lead to the "Rossmann fold" that is often present in proteins that bind nucleotides (especially the cofactor NAD). This is a β-α-β-α-β motif in which the strands form a parallel β-sheet and the helices lie anti-parallel to the strands on one side of the sheet. 78

78 Tertiary Structure A combination of all the secondary structure elements and frequently occurring super-secondary structure elements in single polypeptide chains give rise to the tertiary structure of the protein. Thus the tertiary structure refers to the spatial arrangement of all the amino acids atoms in a single polypeptide chain. 79

79 Domains in the Tertiary Structure A single polypeptide chain can fold into two or more compact, local and semi-independent structural units which are known as domains. Domains range in size from about 25 to 500 residues and are frequently connected by only one flexible segment (in light blue). 80

80 Domains and Sequence Typically, domains are colinear in sequence, but occasionally a domain will have two or more patches of non sequential segments of the polypeptide chain, and hence will have multiple polypeptide links between domains. By following the chain in this example you can see that the central domain (A) is built of two non-sequential segments (red and pink). 81

81 Domains and Function Some proteins have distinct functions for each domain (example gapdh protein visualized below). In other proteins the function is shared between domains. Ligand binding often occurs in the cleft between two domains (see example fpg). gapdh fpg 82

82 New Look on Proteins Levels of Architecture The boundary between secondary and tertiary structure is blurred. Super-secondary elements and domains are intermediate levels between secondary and tertiary structures. For this reason super-secondary elements and domains are sometimes considered to be a subset of the tertiary structure and sometimes a distinct level of the protein architecture. Secondary Super-Secondary 83 Domain Tertiary

83 Blurred Boundaries Not all helices and strands in a protein necessarily belong to a supersecondary element. Although proteins include secondary and tertiary structures, they do not necessarily include super-secondary elements and domains. Furthermore, some elements (such as the 4-helix bundle) can be considered to be a super-secondary element or domain or the full tertiary structure, depending on the context. Super-Secondary Domain Tertiary 84

84 Quaternary Structure 85

85 Quaternary Structure Many proteins, such as the hemoglobin represented here, have more than one polypeptide chain. The different polypeptide chains are called subunits, monomers or protomers. The quaternary structure of a protein refers to the spatial arrangements of its subunits without regard to the internal geometry of the subunit. 86

86 Dimers, Trimers, Tetramers etc... The subunit aggregation leads to the formation of protein oligomers which are named for their number of interacting subunits: dimer, trimer, tetramer, etc... The associated subunits can vary from small dimers such as the HIV-1 protease to very large systems such as this chaperon in GroEL tetradecamer (14 units). dimer tetradecamer 87

87 Homo-Oligomers: Identical Polypeptide Chains The subunits in a protein may be identical. In this case, the resulting homo oligomers are usually symmetrical and almost always exhibit rotational symmetry about one or more axes. Several examples are shown below, according to their symmetry group. C2 D2 C5 D4 88

88 Hetero-Oligomers: Different Polypeptide Chains More than one type of subunit can aggregate together to form the protein unit. In this case it is also common to find multiple copies of various subunits. For example the F1 ATPase has three copies of two different subunits (blue and purple subunits) and three more unique subunits (red, yellow, and green subunits). 89

89 Structural Classification of Proteins 90

90 Structural Classification of Proteins Generally, proteins fall into three main classes, based on their overall 3D structure and their functional role; these are known as Globular, Membrane and Fibrous proteins. 91

91 Globular Proteins Most proteins which are found in the aqueous, intracellular environment or in the plasma are globular. They have a somewhat spherical shape or they are made of several compact domains. 92

92 Hydrophilic Surface and Hydrophobic Core The globular nature of proteins can be explained by their interactions with the surrounding aqueous solvent. Proteins fold in such a way that most residues with non-polar side chains are buried in the center, creating the protein's hydrophobic core (green side chains), whereas most residues with polar side chains remain exposed on the protein surface (yellow side chains). 93

93 Hydrophobic Effect The burial of non-polar residues inside the core of the protein by reducing unfavorable interactions with the surrounding water is known as the "hydrophobic effect". The hydrophobic effect is considered to be one of the most important forces that contributes to the tertiary and also the quaternary structure of globular proteins. The interpretation of this phenomenon is that water-water interactions are the most favorable interactions and in effect, the water squeezes out the hydrophobes so it can interact with itself, leaving the hydrophobes to interact with themselves. 94

94 Membrane Proteins Another class of proteins includes proteins that are attached to biological membranes. The figure describes the characteristic features of the seven transmembrane helix G protein coupled receptors (GPCRs), a family of membrane proteins that cross the cell membrane seven times. They represent an important group of pharmaceutical targets. 95

95 The Lipid Bilayer The biological membranes create the cell's physical barriers and compartments, and regulate the molecular traffic across its boundaries. The membrane architecture is the lipid bilayer in which the lipids' hydrophilic polar heads stick out and the hydrophobic tails form the membrane core. 96

96 Membrane Proteins Types Different proteins associate with membranes to various extents. Peripheral proteins have a fairly shallow penetration of the membrane surface and possess the same structural features as globular proteins. Integral proteins penetrate deep into the lipid bilayer; these proteins have special structural features that will be discussed in the following pages. 97

97 Transmembrane Protein Surface The transmembrane segment of integral membrane proteins must be stable in the hydrophobic hydrocarbon oil-like interior of the lipid bilayer. As a consequence, most of the amino acid side chains that are on the surface of the transmembrane protein must be non-polar (colored in green in the view). 98

98 Transmembrane Protein Folds Furthermore, the polar peptide bond units need to be 'covered' (by creating hydrogen bonds), in order to lower the thermodynamic cost of transferring them to the hydrocarbon interior. This can be achieved either with α-helices (where all peptide bonds are H-bonded internally), or with β-sheet closed structures such as the β-barrel. Currently all transmembrane proteins of known three-dimensional structure correspond to one of these two types. 99

99 Fibrous Proteins Fibrous proteins tend to be long, thin, insoluble in water and arranged to form fibers by associations side by side to construct macroscopic structures - a feature that is important for their structural roles. Most fibrous proteins have regular, extended structures as we will see in the examples that follow. 100

100 Collagen Collagen is the most abundant protein of the human body (it is the matrix protein for bones and skin). Collagen exists as a triple helix in which the individual polypeptide chains helices are very extended (3 Å rise per residue). Each chain is about 1000 residues long (3000 Å in length). The sequence is characterized by glycine residues in every third position, and is also rich in proline residues with about half of their side chains being hydroxylated. Covalent linking of lysine residues between the polypeptide chains enhances the strength of this structure. 101

101 α-keratin α-keratin is used to form hair, fingernails and skin; it can exist as a dimeric or a trimeric α-helical coiled coil. Each chain is made up of about 300 residues (450 Å in length). Disulfide bonds which are formed between Cys side chains enhance the strength of the structure. The coiled coil structure visualized here comes from another protein, tropomyosin, which is present in the muscles. 102

102 Silk Fibroin Silk fibroin is synthesized by spiders for their webs and by silkworms for their cocoons. The architecture of this fibrous protein (made up of β-sheet structures) is illustrated in this theoretical model. The silk fibroin sequence is characterized by specific glycine and alanine rich repeats. Bulky regions with valine and tyrosine residues interrupt the β-sheet stacks and allow for stretchiness. 103

103 Proteins are not Static Proteins are not motionless under physiological conditions. Thermodynamic vibrations of the atoms may induce movement of entire regions of the protein. Dynamic changes of protein conformations range from local side chain rearrangements to complex backbone motions such as the hinge bending illustrated below. Conformational changes are key elements for the biological function of the protein. Hinge movement in Lysine/Arginine/Ornithine binding protein 104