Secondary structure - local folding of the backbone of a linearpolymer to form a regular, repeating structure. For a polypeptide,the secondary structure is determined by the amino acid sequence and the solvent environment in which it is located.

The sequence of amino acids dictates geometric constraints forthe polypeptide. These include maximum lengths betweencovalent bonds, limiting angles in which bonds can be bent, andvan der Waals radii, which limit how tightly structures can bepacked. These factors, along with forces that help preferentiallystabilize structures, such as H- bonds, ionic attractions/ repulsions,hydrophobic interactions, and others, ultimately determine theshape that a peptide has over a short distance. The structureresulting from all these interactions is the secondary structure ofthe protein.

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Secondary structure should not be confused withthe overall shape of a polypeptide. The overallshape of a polypeptide arises from the differentregions of secondary structure folding upon eachother and is called the tertiary structure if itinvolves only the same peptide or the quaternarystructure if it involves two or more separatepeptides.

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Important points:Partial double bond character of the peptide bond. Caused by localization of the pi-orbitals over O-C-N. 3

Alpha-Helix

The alpha-helix and beta-sheet are common protein secondary structures that were originally predicted by Linus Pauling.

The alpha-helix structure repeats after exactly 18 residues, which amounts to 5 turns. It has, therefore, 3.6 residues per turn. Since the pitch of a helix is given by p = nh, we have for the helix, with a rise of 0.15 nm/residue, p = 3.6 (res/turn) x 0.15 (nm/res) = 0.54 nm/turn. Parameters for the other helices shown in Figure 6.3 and Figure 6.4 are listed in Table 6.1.

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In an alpha-helix each carbonyl oxygen is H-bonded to the amide proton on the fourth residue up the helix. Thus, if one includes the H-bond, a loop of 13 atoms is formed. Each of the helices shown in Figure 6.3 and Figure 6.4 has a different number of atoms in such a hydrogen-bonded loop. We shall call this number N. A quick way to describe a polypeptide helix, then, is by the shorthand nN, where n is the number of residues per turn. The 310 helix fits this description; it has exactly 3.0 residues per turn and a 10-member loop. The alpha-helix could also be called a 3.613 helix.

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The alpha-helix repeats after 18 residues, which is 5 turns-therefore 3.6 residues /turn. The pitch of a helix = nh and h= 1.5 /residue = 5.4 /turn of helix.

Idealized helices

The pitch (p) of the helix is the distance parallel to the axis in which the helix makes one turn. There may be an integral number of residues/turn or not.

The rise of the helix is the distance parallel to the axis from the level of one residue to the next.

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The Beta-Pleated Sheet

This is the second famous structure. It is best envisioned by laying thin, pleated strips of paper side by side to make a pleated sheet. Each strip of paper can be envisioned as a single peptide strand in which the peptide backbone makes a zigzag pattern along the strip, with the alpha-carbons lying at the folds of the pleats. This structure can exist in both parallel and antiparallel forms. In the parallel form, adjacent chains run in the same direction- either N-to-C or C-to-N . In the antiparallel form, adjacent strands run in opposite directions.

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Each single strand of sheet can be looked at as a helix with two residues/turn. The H-bonds in this structure are interstrand rather than intrastrand.

H-bonds formed in the parallel sheet are bent substantially. The side chains in the pleated sheet are oriented perpendicular (normal) to the plane of the sheet, extending out from the plane on alternating sides.

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Parallel sheets have a narrower range of allowed dihedral angles than antiparallel sheets. In addition, the parallel sheet structures that form are typically large >5 strands ; antiparallel structures are smaller.

Antiparallel structures are the fundamental ones found in silk, with the polypeptide chains the form the sheets funning parallel to the silk fibers.

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The beta pleated sheet has each residue rotated by 180 o with respect to the preceding one, which is an n=2 helix. Chains can have their NC directions run parallel or antiparallel.

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Hydrogen bonding in beta sheets 12

Note !! The beta strand is an element of secondary structure, while the beta sheet actually involvestertiary structure, since it brings together regionsof the molecule, which may be widely separatedin the primary sequence

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The Beta-turnSince proteins are globular structures, it is evident that the chains have to be able to turn and reorient themselves.The simple beta- bend is one in which the peptide chain forms a tight loop with the C=O oxygen of one residue H-bonded with the amide proton of the residue three positions down the chain.

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RAMACHANDRAN PLOTS:I. THE BACKBONE CONFORMATION IS DESCRIBED BY THE ANGLES OF ROTATIONS AROUND TWO BONDS:

1.THE BOND BETWEEN THE N-ATOM AND 2. THE alpha-CARBON (phi) AND THE BOND BETWEEN THE alpha-CARBON AND THE CARBONYL CARBON (psi). CONVENTION TO DEFINE THE DIRECTION OF POSITIVE ROTATION AND THE 0O VALUE:PRETEND THAT YOU ARE SITTING ON THE alpha-CARBON . POSITIVE ANGLES OF ROTATION ARE CHOSEN FOR THE CLOCKWISE DIRECTION NO MATTER WHICH WAY YOU ARE LOOKING.A VALUE OF 0O CORRESPONDS TO AN ORIENTATION WITH THE AMIDE PLANE BISECTING THE H-C alpha-R (SIDE CHAIN) PLANE AND A CIS CONFIGURATION OF THE MAIN CHAIN AROUND THE ROTATING BOND IN QUESTION.

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The fraction of area that is totally allowed is 7-8 %; partially allowed regions due to conformational flexibility is ~ 22.5%

(II) THE BACKBONE CONFORMATION OF ANY RESIDUE ISA POINT IN phi, psi SPACE. THE RAMACHANDRAN PLOT ISA PLOT OF THESE TWO ANGLES. CERTAIN REGIONS INTHE PLOT RESULT IN ATOMS IN THEIR CHAINSAPPROACHING CLOSER THAN THEIR VAN DER WAALSRADII PERMIT. ONLY A FRACTION OF THE CONCEIVABLECONFORMATIONS IS PERMITTED.

(III) FOR PROTEIN WITH REGULAR SECONDARYSTRUCTURE ALL RESIDUES HAVE EQUIVALENT phi, psiVALUES AND CAN THEREFORE BE DESCRIBED AS A POINTON THE PLOT.

(IV) SIDE CHAIN EFFECTS ARE RELATIVELY SMALL-BULKIER CHAINS RESULT IN SHRINKING ALLOWEDREGIONS.

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Two amide planes are shown; Rotation is allowed around the N-Calpha and Calpha -C=O bonds. These (phi, psi) angles have directions defined as positive rotation shown by the arrows.

Rotation around the bonds in a polypeptide chain

The chain conformation shown here corresponds to an extended structure with both phi and psi = 180 o. 19

The C=O oxygen (residue I-1) and the H atom on residue I+1 overlap. Therefore this pair of angles

is disallowed.

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This comparison is for predictionof the secondary structure of BPTI

The Chou-Fasman rules are compared with the secondary structure deduced from the X-Ray data. The agreement is good.

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The phenomenon of circular dichroism is very sensitive to the secondary structure of polypeptides and proteins. Circular dichroism (CD) spectroscopy is a form of light absorption spectroscopy that measures the difference in absorbance of right- and left-circularly polarized light (rather than the commonly used absorbance of isotropic light) by a substance. It has been shown that CD spectra between 260 and approximately 180 nm can be analyzed for the different secondary structural types: alpha helix, parallel and antiparallel beta sheet, turn, and other. In fact, optical rotary dispersion (ORD) data suggested a right-handed helical conformation as a major protein structural element before the Pauling and Corey model and Kendrew's structure of myoglobin. Modern secondary structure determination by CD are reported to achieve accuracies of 0.97 for helices, 0.75 for beta sheet, 0.50 for turns, and 0.89 for other structure types

In proteins the aromatic bond structures are of importance in spectroscopy. For protein structure studies we are primarily concerned with backbone conformations. The peptide bond amide group is the dominant chromophore of the polypeptide backbone and has a weak absorption maxima at 220nm and a stronger absorption maxima at 195nm. Circular dichroism makes use of the fact that right and left handed polarized light are absorbed slightly differently in asymmetric molecules. Even though individual amide groups in protein backbones have a symmetric transition dipole, their mutual interaction in highly oriented secondary structures induces asymmetries which translated into circular dichroism spectra (difference of absorption of left and right handed polarized light not zero). Protein secondary structure can be revealed based on their characteristic electronic circular dichroism behavior between 190 and 220nm. 30

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Circular dichroism to study secondary structures of proteins

Amino acids are optically active molecules and in a polypeptide are often found as part of regular secondary structures. The frequent occurrence of alpha helices and beta sheets in proteins has thus been exploited by measuring the presence of such regularly arranged units from circular dichroism spectra of protein solutions. Although CD measurements are not useful to obtain high resolution structures, but merely secondary structure content of a protein, this information is useful to study the status of protein folds. It can generally be assumed that the absence of any alpha helical or beta strand components indicate the unfolded state of a protein.

Dichroism occurs when light absorption differs for different direction of polarized light. Light can be polarized either in a linear way, where the plane of the electric vector is fixed while its amplitude oscillates, or in a circular way, where the plane of polarization of the electric vector is modulated while the amplitude remains constant. The electric vector of circularly polarized light describes a helix which may be right-handed or left-handed.

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Circular Dichroism spectra of poly-L-lysine in the alpha-helical, beta-sheet and random coil conformations as indicated. Similar spectra may be obtained for other polyamino acids, so they reflect backbone secondary structures, primarily.

Spectra of proteins may be analyzed to determine the amount of these three conformations that are present.

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Cartoon drawings of: A) triosephosphate isomerase (H:0.52, S:0.14, T:0.11, O:0.23); B) hen egg lysozyme (H:0.36, S:0.09, T:0.32, O:0.23); C) myoglobin (H:0.78, S:0.0, T:0.12, O:0.10); and D) chymotrypsin (H:0.10, S:0.34, T:0.20, O:0.36). Secondary structures are color coded red:helix. green:strand, and yellow:other.

FT-infrared spectroscopyLike circular dichroism analyses of proteins, Fourier transform infrared (FT-IR) spectroscopic studies and are easily performed and require relatively small amounts of material (~0.1 mg). The infrared spectra of polypeptides exhibit a number of so-called amide bands which represent different vibrational modes of the peptide bond. Of these, the amide I band is most widely used for secondary structure analyses. The amide I band results from the C=O stretching vibration of the amide group. These vibrational modes, present as infrared bands between approximately 1600-1700 cm-1, are sensitive to hydrogen bonding and coupling between transition dipole of adjacent peptide bonds and hence are sensitive to secondary structure. A critical step in the interpretation of IR spectra of proteins is the assignment of the amide I component bands of different types of secondary structure. Amide I bands centered around 1650-1658 cm-1 are generally considered to be characteristic of alpha helices. Unordered structure and turns also give rise to amide I bands in this region complicating analyses. Beta sheets give rise to highly diagnostic bands in the region 1620-1640 cm-1. Parallel and antiparallel beta strands are distinguishable only as antiparallel strands contain a large splitting of the amide I band due to the interstrand interactions. Water (H2O) also has an intense IR band in the region of the amide I band and requires that samples are measured in 2H2O or that the solvent resonance is subtracted (digitally).

The IR spectrum of peptides and proteins is fairlysensitive to secondary structure. IR spectra acquiredwith polarized radiation provide information aboutthe orientation of the absorbing groups.

The vibrational modes of the peptide bond shownabove are: N-H stretch ~3300 cm-1

C=O stretch ~ 1650 cm-1

Mixed C-N stretch and N-H in-plane bend ~ 1550 cm-1

The C=O stretch of the side chain appears at 1734 cm-1

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Secondary structure sensitivity:alpha helix 1650beta sheet doublet 1620(s), 1690 (w)

Secondary structure from FT-IR spectraNumerous attempts have been made to extract quantitative information on protein secondary structure from analyses of these amide I bands (for reviews see Byler & Susi, 1986;Surewicz, et al, 1993). Both curve-fitting and pattern recognition techniques have been applied with varying success. Since the potential sources of error in CD and FT-IR analyses of secondary structure content are largely independent, the two methods are highly complementary and could be used in conjunction to increase accuracies. Despite limitations in the quantitative assessment of protein secondary structure content, FT-IR (like CD) provides a good tool to monitor conformational changes in polypeptides and proteins

NMR spectroscopyIn the past 20 years, nuclear magnetic resonance (NMR) spectroscopy has proved itself as a potentially powerful alternative to X-ray crystallography for the determination of macromolecular three-dimensional structure. NMR has the advantage over crystallographic techniques in that experiments are performed in aqueous solution as opposed to a crystal lattice. However, the physical principles that make NMR possible, limit the application of this technique to macromolecules of less than 35-40 kD. Fortunately, a large number of globular proteins and most protein domains fall into this molecular weight regime. It is possible to determine the secondary structure of a protein using NMR techniques without determining the three-dimensional structure. Of the three most commonly used methods of secondary structure determination not requiring a three-dimensional structure, NMR is potentially the most powerful. Unlike secondary structure determinations by CD and IR which provide overall secondary structure content (% helix, % sheet, etc.), using NMR parameters, secondary structures are localized to specific segments of the polypeptide chain. However, obtaining secondary structure from NMR data requires considerably more material (milligrams) and effort (requires sequence specific resonance assignments) than the other spectroscopic techniques and is limited to proteins of molecular weight amenable to NMR investigation (<35-40 kD).

Sub-atomic particles (e.g., proton, neutron, electron, etc.) possess a characteristic called spin angular momentum. From quantum mechanics, each particle has a spin value of 1/2. The combination of multiple particles in the nucleus results in an overall spin property for each atomic isotope. Those isotopes with an even number of protons and neutrons will have zero magnetic spin (e.g., He-4, C-12 and O-16). An odd number of protons and an even number of neutrons (e.g., H-1, N-15, or F-19) or an odd number of neutrons and an even number of protons (e.g., He-3, O-17 or Ca-41) result in an overall (multiple of 1/2) spin. Those isotopes with odd numbers of both protons and neutrons (e.g., H-2 or N-14) have more complex spin states and are less suitable for direct NMR observation in macromolecules. Fortunately, each of the four most abundant elements in biological material (H, C, N, and O) have at least one naturally occurring isotope with non-zero nuclear spin and is in principle observable in an NMR experiment. The naturally occurring isotope of hydrogen, H-1, is present at >99% abundance and forms the basis of the experiments described here. Other important NMR-active isotopes include C-13 and N-15 present at 1.1 and 0.4% natural abundance, respectively. The low natural abundance of these two isotopes makes their observation difficult on commonly isolated natural products. These two nuclei are however very extensively used for larger (>10 kD) proteins which can be isotopically enriched (to >95% if necessary) when cloned into over expression systems.

In the presence of an external magnetic field, the spin angular momentum of nuclei with isotopes of overall non-zero spin will undergo a cone-shaped rotation motion called precession. The rate (frequency) of precession for each isotope is dependent on the strength of the external field and is unique for each isotope. For example, in a magnetic field of a given strength (e.g. 14.1 Tesla) all protons in a molecule will have characteristic resonance frequencies (chemical shifts) within a dozen or so parts per million (ppm) of a constant value (e.g., 600.13 MHz) characteristic of the particular nuclear type. These slight differences are due to the type of atom the proton is bound (e.g., C, N, O, or S) and the local chemical environment. Thus each proton should, in principle, be characterized by a unique chemical shift. In practice, this is never observed as some protons such as the three protons of each sidechain methyl group of Thr, Val, Leu, Ile, and Met and most pairs of equivalent (2,6 and 3,5) aromatic ring protons are found to have degenerate chemical shifts. Other protons (e.g., some OH, SH, and NH3) are in rapid chemical exchange with the solvent and thus have chemical shifts indistinguishable from the solvent resonance. Nevertheless, nearly complete chemical shift assignments are often possible and are a prerequisite for structural studies by NMR.

Structural information from NMR experiments come primarily from through-bond (scalar or J coupling) or through space (the nuclear Overhauser effect NOE) magnetization transfer between pairs of protons. J couplings between pairs of protons separated by three or fewer covalent bonds can be measured. The value of a three-bond J coupling constant contains information about the intervening torsion angle. This is called the Karplus relationship and has the form: 3J = A cos (theta) +B cos2 (theta) + C where A, B, and C are empirically derived constants for each type of coupling constant Unfortunately in general, torsion angles cannot be unambiguously determined from a Karplus-type relationship since as many as four different torsion angle values correlate with a single coupling constant value as seen below. Similar relationships can be determined between the three-bond coupling constant between the alpha proton and the beta proton(s) yielding information on the value of the sidechain dihedral angle chi1. Constraints on the dihedral angles phi and chi1 are important structural parameters in the determination of protein three-dimensional structures by NMR.

The other major source of structural information comes from through space dipole-dipole coupling between two protons called the NOE. The intensity of a NOE is proportional to the inverse of the sixth power of the distance separating the two protons and is usually observed if two protons are separated by < 5 Angstroms. Thus the NOE is a sensitive probe of short intramolecular distances. NOEs are categorized according to the location of the two protons involved in the interaction. Intraresidual NOEs are between protons within the same residue whereas sequential, medium, and long range NOEs are between protons on residues sequentially adjacent, separated by 1, 2 or 3 residues, and separated by four or more residues in the polypeptide sequence. A network of these short inter-proton distances form the backbone of three-dimensional structure determination by NMR.

Hydrophobic residues sequester inside ofglobular proteins-a result of the hydrophobic effectHorse Heart Cytochrome C

Red = hydrophobic residues, Green = Hydrophilic residues39

Collagen:- Rigid, inextensible fibrous protein -principal constituent of connective tissue

(tendons, cartilage, bones, teeth, skin and blood vessels).- basic structural unit is tropocollagen

(three intertwined polypeptide chains of ~1000 amino acids,molecular weight of 285,000)-tropocollagen is 300 nm long and 1.4 nm in diameter.-Primary structure: high gly (1/3 of the amino acids) and pro.-uncommon amino acids are also found in the structure, 3- and 4-hydroxyproline, and 5-hydroxylysine (G and G 174).-higher order of structure. Staggered arrays of tropocollagen formorganized fibrils giving rise to a characteristic banded pattern inEM studies.

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α-KERATIN

-dominated by alpha-helical segments of polypeptide-amino acid sequence is a central alpha-helical rich domain of 311-314residues flanked by non-helical – and C-terminals of varying size andcomposition.-typical structure: 4 helical strands aranged as twisted pairs of twostranded coiled coils.-primary structure is a quasi-repeating 7 residue segments of the form(abcdefg)n . These units are not true repeats but a and d are usually non-polar amino acids which must be, and are buried in the rope likestructure-In some forms of keratin, S-S bonds form between cysteine residues ofadjacent molecules, making the structure insoluble.

-occurs in claws, fingernails, hair and horns.The S-S bonds may be reduced and cleaved in hair-then reoxidized andre-formed to change the curl or wave (“permanent”).

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Type structures of globular proteins-Notation devised by Jane Richardson

Blue spirals-alpha helicesOrange segments beta sheets

Arrow heads at the end of beta strandspoint in the N C direction

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Regions of secondary structure are themselves folded into specific compact structures of the whole polyypeptidechain. Each atom occupies a specific position. This is known as tertiary structure.

N.B. Each copy of a native protein molecule has approximatelythe same three dimensional structure as all other copies.

This is not the case for synthetic polymers where there is usually a statistical distribution of conformations present in solution.

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Helical Wheel Plots

To construct a helical wheel plot, a projection of the residues in a helix is made along the helical axis onto the X-Y plane. In an alpha helix, the helix repeats every 3.6 residues. Thus, each residue is 100o from its neighbor.

Example:The myoglobin E Helix sequence:SEDLKKHGATVLTALGGILThe helical wheel plot shows that the hydrophobic residues are concentrated along one side of the helix. This is theside of the helix that faces the hydrophobic core of the protein

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Ribbon diagram of the bovine pancreatic trypsin inhibitorbackbone and the three disulfide bonds.

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Diagram of the hydrogen bonds between polypeptidebackbone atoms of BPTI. 55

Carbonic anhydrase polypeptide chain. The C-terminal is inserted through the plane of other segments of the polypeptide chain. A a knot would result if it were pulled downward. The white ball in the middle is a Zn2+ bound to the protein through the imidazole side chains of three His residues.

Zinc ion

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The four internal water molecules of BPTI are marked( orange arrow ) pointing to their O atoms.The water molecules pair with internal polar groups in the protein

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Generic energy level diagram for electronic spectroscopy-called a Jablonski diagram. S= singlet states (paired electrons;T= triplet states (unpaired electrons)

Absorption within the ground electron state constitutes theIR process. Raman scattering is not shown.

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Energy Transfer-Schematic of Processes

Energy Transfer as a Spectroscopic ruler

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Energy Transfer-Equations !!!!!

Efficiency of transfer = ro6/ (ro

6 + r6 )

Where r = distance between donor and acceptor ro

= characteristic distance for the donor acceptor pair that depends on spectroscopic parameters of the donor and accptor

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Classes of Protein Structures:

1. alpha-mostly alpha-helical (4 helix bundles)2. beta-mostly beta- sheet (barrels)3. Alpha,beta-repeating alternating helix and sheets4. alpha+beta- segregated helix and sheets.

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Beta-alpha-beta motifs

Antiparallel beta-strands can be linked by short lengths of polypeptide forming beta-hairpin structures. In contrast, parallel beta-strands are connected by longer regions of chain which cross the beta-sheet and frequently contain alpha-helical segments. This motif is called the beta-alpha-beta motif and is found in most proteins that have a parallel beta-sheet. The loop regions linking the strands to the helical segments can vary greatly in length. The helix axis is roughly parallel with the beta-strands and all three elements of secondary structure interact forming a hydrophobic core. In certain proteins the loop linking the carboxy terminal end of the first beta-strand to the amino terminal end of the helix is involved in binding of ligands or substrates. The beta-alpha-beta motif almost always has a right-handed fold as demonstrated in the figure.

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Simplest way to pack helices: antiparallel manner, with a slight left-handed twist ofthe helix bundle. Mostly these occur as four-helix bundles. Example is tobacco mosaic virus protein.

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The leucine zipper arises from the periodic repetition of Leu side chains from the same side of the helical cylinder, where they can enter into hydrophobic interactions with a similar set of Leu side chains extending from a matchinghelix in a second polypeptide. The motif appears in protein dimerization.

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Helix-turn-helix

The loop regions connecting alpha-helical segments can have important functions. For example, in parvalbumin there is helix-turn-helix motif which appears three times in the structure. Two of these motifs are involved in binding calcium by virtue of carboxyl side chains and main chain carbonyl groups. This motif has been called the EF hand as one is located between the E and F helices of parvalbumin. It now appears to be a ubiquitous calcium binding motif present in several other calcium-sensing proteins such as calmodulin and troponin C.

EF hands are made up from a loop of around 12 residues which has polar and hydrophobic amino acids at conserved positions. These are crucial for ligating the metal ion and forming a stable hydrophobic core. Glycine is invariant at the sixth position in the loop for structural reasons. The calcium ion is octahedrally coordinated by carboxyl side chains, main chain groups and bound solvent.

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Postranslational Modifications:

1. Deacylation, acylation of N-terminus2. Proteolysis3. Methylation4. Phosphorylation5. Sidechain modification for cross-linking6. Conversion of sidechains to prosthetic groups7. Attachment of prosthetic groups8. Attachment of lipids9. glycosylation

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Symmetry:

-Proteins with globular subunits are usually arranged with a high degree of symmetry

-near-symmetry or absence of symmetry may suggest a regulatory role

-fibrous proteins are less symmetrical and are composed of less symmetrical subunits.

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LAST LEVEL OF PROTEIN STRUCTURE: QUATERNARYSUBUNITS - SPECIFIC AGGREGATES OF TWO OR MOREPOLYPEPTIDE CHAINS. INTERACTIONS BETWEEN FOLDED POLYPEPTIDE CHAINS INMULTISUBUNIT PROTEINS ARE ALL OF THE SAME WEAKINTERACTIONS WE HAVE DISCUSSED PREVIOUSLY.INTERACTIONS BETWEEN IDENTICAL SUBUNITS RESULT INSOME TYPE OF SYMMETRIC STRUCTURE.

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THE LANGUAGE USED TO DESCRIBE THE SYMMETRY OFTHESE STRUCTURES - GROUP THEORY- THE PARTICULARSYMMETRY ARRANGEMENT IS CALLED THE POINT GROUP.PARTICULAR POINT GROUPS ARE DEFINED BY THEIRCOLLECTION OF SYMMETRY ELEMENTS.(1) AXIS OF SYMMETRY- An N-FOLD AXIS OF SYMMETRY ISPRESENT IN THE SYSTEM IF A ROTATION OF THESTRUCTURE BY 360/N DEGREES PRODUCES A STRUCTUREINDISTINGUISHABLE FROM THE ORIGINAL.

3 FOLD AXIS = ROTATION BY 1200 .

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Quaternary Structure of collagen

-Assembly of triple helices into microfibrils

-Interactions between triple helices produce arrays of parallel molecules with a stagger of 234 residues (674 )

-After assembly, the structure is stabilized by a wide variety of covalent cross-links between the triple helices n involving primarily the hydroxy-lysine side chains.

In bone-collagen provides a matrix that is cemented in a rigid structure by deposits of crystals in a poorly crystalline phase of hydroxyapatite: (Ca)10(PO4)10(OH)2

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DIMERS - MOST COMMON FORM OF INTERACTION.OFTEN DIMERS HAVE FURTHER INTERACTIONS AND GIVE RISE TO STRUCTURES OF HIGHER SYMMETRY. THE OCCURRENCE OF THREE MUTUALLY PERPENDICULAR TWO FOLD AXES IS COMMON. THIS CORRESPONDS TO THE D2

POINT GROUP.MOLECULES EXHIBITING THIS TYPE

OF SYMMETRY HAVE A WELL-DEFINED (SMALL)NUMBER OF SUBUNITS

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SOMETIMES >1 TYPE OF POLYPEPTIDE CHAIN IS INVOLVEDIN INTERACTIONS TO PRODUCE SYMMETRY. HEMOGLOBINIS MADE UP OF TWO TYPES OF CHAINS, alpha AND beta. THEINTACT STRUCTURE CONSISTS OF TWO OF EACH CHAIN,AND IS REFERRED TO AS AN alpha2 beta2 DIMER. THE MOSTIMPORTANT CONTACTS IN THE STRUCTURE ARE BETWEENalpha AND beta, RATHER THAN alpha,alpha OR beta, beta.IT TURNS OUT THAT THESE INTERACTIONS BETWEENSUBUNITS CONTROL THE PROTEIN FUNCTION.

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Subunit-subunit interactions

-the hydrophobic effect-H bonding (sheets)-helix stacking-salt bridges-S-S bond-metal ions

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