units protein teins of the carry to nthe ing their gto shall Iwill sof ‘of the Figure 1 Feprosertaton ofa polymer by a Succession ofaiome 0UpS Ay Ay A. Geometry of a polymer chain ‘Torepresent a polymer in space, we shall first consider only the main backbone of | the macromolecule: for example, the chain of carbon atoms in polyethylene, the peptidechain in proteinsor the phosphodiester chain in aueleicacids, Thisamounts tosaying thatall such polymers have in common small number of parametersand intrinsic properties characteristic oftheir geometry. For this purpose, the sequence ‘of monomersisrepresented by aset of vectors fj...» joining theatomsor groups ‘of atoms represented by points Ay. Ay,A>,... (Fig. 1.1). The ith bond links the (/—1jthatomand the th atom and ischaracterized by the vector J,with magnitude 4a, The set of n vectors J,characterizes the molecule consisting of n+ I)atomsata given instant. In the absence of any data about the relations existing between these ‘various vectors, the macromolecule can only be described statistically by general geometrical parameters, 1.1 Distance between the ends of a chain The vector r connecting the two ends of the chain is given by ye a For a purely statistical description, we require a scalar mean value, such as the square ofthe distance between the ends: Peers Died10 MOLECULAR BIOPHYSICS ‘Alongside the squared terms J, f,= in the scalar product, the cross-products, J -Tyappear twice, so that LexDny, (12) by including only one (pur, that for which , and fora given relative rotation of C, ‘and C, the value and sign of © remain the same. In both eases (cis and trans) the four atoms C), Ca. Cs, Cgare in the same plane. As well as these 1wo eclipsed positions, two staggered positions are possible, as in ‘organic chemistry. With the same sign conventions. these will be called gauche-plus (gauche+ or g”) oF gauechesminus (gauche or g~) depending on whether the rotation from the position cis (9 = 0) ismade towards the right or towards the lef. Se Cy iheangl ean be deten To illus thedifferent freely on the vector Phase to rotate on fra hea=t therefore ha Whensubs segments sep aren k pi ‘The calcula In becomes the first. In (-y=3a throe times g In order te include the f1.3. CONSTRAINTS ON THE VALENCE BOND te angles made by successive bonds are known, the sealar product I. = cos" &. For the two bonds i and j we therefore have (with j > hae cose (9) When substitutingeqn 1.9intoegn 14, wehave to takeintoaecount the numberof segments separated by the same number/— =k, Ithechain has n segments there aren ~ k pairsof this type. Carrying out the substitution and putting x = cos gives 428 Mn 4) (1.10) e ‘The caleulation of 7°) (Box 1.2 leads tothe final expression: (P) = na?I(1 + 2)/(1 = x) — 2x1 — x*)/n(1 ~ 7] aa) In becomes larg, the second term on the right becomes neaigble compared with the first, In that case, if we assume that x=0.5 (= 60"), the term (1+ s)/ (1x) = Band the mean square ofthe distance between theends ofthe chainis now three times greater than that of a Gaussian chain of the same length. In order to get closer approximation to real macromolecular chain, we must include the fact that there are limits to the rotation around the valence cone. 314 lo? ad 1-cos3¢ 1400830 Figures.6 Thepostons otthemnmain thelunctonsi —cos3eandt + cos30. MOLECULAR BIOPHYSICS The probability of « conformation characterized by angles 6.02.03..-. will depend on the potential energy E40... 02...) of the molecule for this con- figuration, and more specifically on the Boltzmann factorexpl—Eo(01.03.0s.---¥/ {eg7]. where ky is Boltzmann’s constant (a notation used throughout the book t© distinguish it from other uses of the symbol k). 14 Torsional potential Here again, a simplified model will enable us to gain a better understanding of the way to tackle the problem. Take the case of chain of four earbon atoms. The rotation ofC, with respect to Cis deseribed by an angle around C:C,(oragain by the dihedral angle between the two planes C\C:C3 and C:C\C,), Experiment indicates that all values of @ are not equally likely. In other words, the potential function £y(6) has one or more minima separated by potential barriers. The Boltzmann factor exp{—Ex(o) ky) is @ maximum in the potential wells. As a result the molecule will spend most ofits time in one of the configurations corre- sponding to-a minimum in Ep. There are thus several rotation isomers or rotamer. The probability of finding the molecule outside one of these states is virtually negligible, ‘The situation is obviously more comple if the Four carbon atoms form part ofa Jongehain, Because of interactions between atomic groups, the minimum values of pare different but the general result remains. The function Fp representing the potential nergy of rotation or the sorsianal potentialcan therefore be described by ‘combinations of trigonometsc functions. ‘The expression generally used is of the form Ep(o) = (V/2)(1 £080) (2) ‘where mis the multiplicity of potential wells and the + or ~ sign corresponds toa {avoured eclipsed or staggered position respectively. Vis the height ofthe potential barrier (e-. in keal mol”) ‘The function 1 +cos3o bas three minima at @= 60°, 180° and 270°, For 1-030, the minima are at 0°, 120° and 240°, The representation in Fig. 1.6, similar to the Newman projection, indicates the privileged positions, ie. the loca- tons ofthe various rotamers, In order to analyse what happens with a large number of bonds and atoms, we ‘must examinein more detail the variousinteraction energies between the atomsof'a sven macromolecule.Intermolecular forces 2.1 Introduction “The simplest way to represent intermolecular forces is to start by considering two atoms A and B capable of forming a molecule AB, such as Cl and H to form HCL When A and B ae sufficiently far from each other (theoretically at infinity), the energy of the two-atom system is the sum of the energies Ey and Ey ofthe atoms taken separately. When A and Bare separated by a distance a potential energy of interaction Fy{r) must be added to the total energy. £y(") is the work done in bringing the atoms from infinity to thei final positions and is therefore given by ‘where F(r) is the force exerted between A and B. By convention, a repulsive force is counted positive and a ve force negative. Differentiating both sides ofeqn 2.1 leads to the usual relationship defining force in terms of potential energy Fir) =~ dE p(r)/dr (22) ‘or, more generally, ~ erad Ep (23) The components ofthe vector gradient (grad) are the partial derivatives of Ey with respect 1 each of the coordinates being used inthe general problem. Equation 2.2 is appropriate when the two atoms or two molecules (forming two assemblies of atoms) have spherical symmetry. AS soon as the relative orientations of the molecules themselves are Tavolved, only eqn 2.3 is valid . ae . Ot 2.2 Electrical origin of the interaction energy “The neaction eneray between molecules i de to eet frees. the charge disrbtion na moleulzis known rom wavefunction solutions of Sebringer’s austin, Kis paable a pricpl to ealculae the eaceay by supepostion ef, MOLECULAR BIOPHYSICS Coulomb potentials using the Hellmann—Reynuman theorem ria= [fee mledote) any 24) Where ands are the position vectorsof the elementary charges pr) dr distributed ‘over molecules I and 2. This type of calculation ean be carried out by computer provided we have a precise knowledge of both the atomic structure of each molecule and thei relative geometrical configuration. Several factors are, however, ignored in such a calculation: (1) the deformation of the orbitals of one molecule in the electric field created by a neighbouring one; tid vice {@)_ Brownian motion, which changes the respective postions of the molecules and leads to the replacement of instantaneous magnitudes by mean vales: (3) charge Muctuations on each molecule Becauscof these complications, clas formule for interaction energie between charges nd dipole moment (permanent, induesdand spontaneous) are sil used, and have the advantage of providing an analytical expression forthe energy (Our tasks therefore to call the potential W produced By a general change distribution ican be shown (ce Box 21) that this ven by the sum ofthe petals produced by a charge a dipole, a quadrupole, ec. To begin wih, we Shall estitourslies tothe chargecharge. charge~dipole and dipole-dipole interactions. (Charges will represent fre ions or ionized. groups in «biopolymer. Dipoks correspond to ssymetrcal charge distributions such asthose in 0,3 pepide,a Purine orpyrimidine base or an aminoacid, Ia thesecases, the molecules to $e polar and has a permanent less dipole momen. “The potential energy ofa charge qs given by the product ofthe charge and the potential Wat the postion i occupies: Seay a \fe= av es) ‘The potential energy ofa dipole isthe negative sealar product ofthe ipolemoment and the electric field E atthe dipole: pap E (26) (see eqn 15.15). 2.3 Interactions between charges and permanent dipoles 23.1 lon-ion ‘The interaction energy Ep between two ions with charges q, and > separated by a Aistance ris given by Coulomb's aw Fe = qiqn/4necor (27) pispreater than Orepulsiveenergy)ifqy and qs have the same sgn, and ess than 0 {attractive energy) if they have opposite signs; = isthe dielectric constant of the ‘medium,\ 2.3 INTERACTIONS BETWEEN CHARGES AND DIPOLES 7aM @ P ° Figure 21 Geomery tthe neracton between a dpole at O and anion at M MOLECULAR BIOPHYSICS Inmany cases, itis difficult to assign a value to =, particularly near charges. Inthe rest ofthis chapter, therefore, all expressions will be written with ¢~ I (vacuum), {knowing that for other media we only have to replace by £9 (see Part IV). 232 lon-dipole Ifa molecule with a permanent dipole moment p is located at a point where the cleetrie field due to-an ion is E, then it has an energy Ep =p E=-pE cos where is theangle between the direction ofthe dipole moment and the line joining, the centre ofthe dipole O to the ion of charge atthe point M (see Fig. 2.1), Since the field E produced by a charge g ata distance ris E=ug/srey here wis a unit veetor along OM, then Ep =pqeost/4ney? (28) Ifthe moteculeis undergoing Brownian motion, then all possible orientations of ‘are possible. The statistical weight of dipoles making an angle # is given by the Boltzmann factor: exp(—Ee/kuT) = exp(pE eos 4/kn7) ‘The probability that the vector plies between two cones with semi-vertical angles @ and 0-+d0 is sin @d8)2. The projection pos of the dipole moment on to the direction ofthe Field E thus has the mean value Jexp(pEcos0/ky7ypcos0sinoae/2 ) =*— Fes pEcos/kT) sin 0d/2 Putting pé/ky?- this becomes a standard calculation (see Box 15.2) and gives (p) = pew) where £(x) = eoth x I/x Mp E kyT,the dipole takes up a direction near the position corresponding to minimum energy, ie. @ = 0, ain: ree ‘This is a situation encountered in the hydration of ions. The permanent dipole ‘moment of H,O takes up @ mean position in the radial direction of the field of theion, 233. Dipole-dipole Itcan be shown see Box.) that the interaction energy between twodipolesp and ‘Ps separated by a distance ris Ep = pips) 40° @uy where K= sind sin scos{o, 3) 2e0s cosa. The angles #82. d1. 62 are defined in Fig. 2 If both dipoles are undergoing Brownian motion affecting their rotation (the angle 6) but not the distance r, then a mean value for K must be calculated. Assuming that (Ep) < kT its found that the mean value (Ep) is given by 2) Sky TA)" 2.12) ‘The interaction energy thus varies as 1/* (and no longer as 1//* as it does in the absence of motion. 2.4 Induced dipoles So far, we have been considering interactions between charges. dipoles et. that exist in the molecules from the start without any external clectrial influence. However, as soon as a collection of atoms is placed in an electric field E, their ‘charges (mainly electrons) are displaced and the molecule is polarized, producing an induced dipole (see section 15.3). The moment p of the dipole is related to the field Eby p= aE (213) where ais the polarizability of the molecule, assumed toa frst approximation to be 4 scalar quantity characteristic ofthe molecule and proportional to the molecular volume (a has the dimensions of a volume). 19 Figure2.2 Geometrical paraneterstor ‘spole-cpoleitracion a20 MOLECULAR BIOPHYSICS 2.4.1 ton- molecule interaction ‘ol of Drud ‘Tho enery Ep ofthe induced dipole placed in the inducing field Bis oa a4 cae whereit witha Pe2.4 INDUCED DIPOLES When the fsld Eis due to. charge g then B= q/drey? siving ‘ fe ‘This energy is always due to an attractive force and varies as I/r* 2.42 Dipole-molecule interaction The field £ produced at point P (Fig. 2.3) bya dipole of moment pp at a point © has two components (se section 15.2.1) E \where isthe distance OP and 0s the angle between the dipole and OP. Sill assuming that the molecule is isotropic with a scalar polarizability a, the ‘energy will depend on the field £ given by 0 /(4re9)"2 1s 2prcosd)/Axcor Ey =(pysind)/4rcor (2.16) = (Aeos? 0+ sin? op} (Arco) a7 and, from eqn 2.14, the energy will be Ep = ~eya( 30s? + 1)p/204ney)*# ay) I the molecule and/or the dipole are undergoing Brownian motion, the spatial ‘mean of ¢0s°0 (Le. 1/3) is the appropriate value, and hence Fe 0040 (2.19) If the molecule is anisotropic, the contributions from each component of the field and the value ofthe polarizability in the directions of each component must be used. However, although this calculation givesa different value for the numerical ‘coefficient of Ey. it does not alter its dependence on r-* and py? 243 Interaction between two induced dipoles Thistype of interactions present forall molecules since it arises from fluctuations in electron density. which, at any given moment, create an instantaneous dipole ‘whose external field induces a dipole in a neighbouring molecule. From the above calculation, the interaetion energy is proportional to the inducing field and, since thisvariesas IP. the energy will aryas /#°. Anexactcaleulation of Eycan only be carried out by applying quantum mechanics. It should, however, be pointed out thatthe frequency of the uctuations is very high and that as result, the polat- zabilty is no longer a statie quantity but is related to the motion of the electrons under the action of an electromagnetic felt in the optical region ofthe spectrum, Because ofthis, the interaction forces are als called dispersion forces since they can be related to interactions between radiation and matter, the provinee of the ‘theory of dispersion of light in material media, By combining the classical theory of Drude with a quantum treatment of the harmonic oscillator. itis possible to caleulate Ey. The results Ep = ~Snyvrayaz/2ir4 +2)" (2.20) ‘where it isassumed that each molecule can be represented by a harmonic oscillator with a natural frequency 1) and vsand static polarizabilities, and a (his Planck's ° a Figure 2.2 Gecmsrca parameterstor ‘p08 -maleoule inaction a2 MOLECULAR BIOPHYSICS constant, Ifthe two molecules are identical then shi aes ean p= As the distance r between the oscillators increases, the electromagnetic field produced by one of the instantaneous dipoles takes time = re to propagate, where cis the speed of light. Asa result, the interaction with the second induced. dipole only occurs after a time 2r/c, I the first dipole has had time to change its direction during this period of time, the interaction energy is reduced, which emphasizes the ‘short-range’ nature ofthis type of interaction. |A semi-empirical formula obtained from quantum mechanics is often used instead of eqn 2.20. If / and />are the ionization energies ofthe molecules, then itis found that Fp = —Sylzayas/2h + hy (222) 2.5 Forms of potential energy 25.1 General table we put C= (4ne9)"! =9 « 10” SL units the various forms taken by the potential ‘energy can be summarized asin Table 2.1. It can be checked that every expression, hhas the dimensions of energy, ML°T.*, remembering that =» itself has dimensions of M-'L*TQ®, It ean also be seen that a1 law typical of Coulomb potential is, replaced by a I/F" law with 4 ‘Thisisthey built, each equal to th (see Chapt 2.6 The Alongside form for & which Ep « Invdrogen completely2.6 THE HYDROGEN BOND large repulsive forces between electron clouds coming into contact. The one most frequently used isthe Lennard-Jones potential (Box 23): Eplr) = Ealvo/0)!® ~ 2 olr0/) (2.2) where the term ine! passes through a minimum (4 rary = 089% (Fig. 24) Inmany cases, however. an even simpler form is used for Fy(r) by assuming that the molecules can be modelled by hard spheres of radius 8 ifrem Eo © ifr>m Fu =0 ‘Thisis the potential implicitly used wen so-called “compact” molecular models are built, each atom being represented by a sphere or part of a sphere with a radius equal to the ‘van der Waals radius’. The method for determining conformations (ee Chapter 5) also depends on this simplified model of molecular contacts, is a short-range repulsive potential. This function and Ep = ~ Ey) for r=. Its zero for 26 The hydrogen bond Alongside the above interactions between molecules, which lead to an analytical {orm for Ep by classical methods, there is another type of intermolecular bond for which Zp can no longer be considered as 2 spherically symmetric function: the Inydrogen bond. The interaction in thiscase is directional and it can only be studied completely by using quantum mechanics. 23 X= Figure 24 Potent wth spherical ‘5mm indeed coordinates: {a} Lennard-tones potent (b) hard sphere peter¥. MOLECULAR BIOPHYSICS 26.1. Definition and properties “The term hydrogen bond denotes a particular type of interaction occurring between proton donor group D, whichisstrongly polar. such as FH, OH, NH, SH.ete.,and ‘a proton acceptor atoms A, which is strongly electronegative, such as F.O. N. ete ‘Theclectronegativity in the later case arises through the presence of electron pairs that, for most ofthe time, are not involved ina covalent bond, asi R RN So RON R,~ Ro ‘The bond is ofthe form D-H---A. The distance between Dand A depends on the two atoms involved. For F—H--F it is 2.25 A, for O-H- 0 it is 2.75 A and for N-H--Oitis2.9-30A, AL Tits sight, this“attraction’ of the proton looks similar toa simpleelectrostat typeof foree, which might providea simple description ofthe bond. Insucha simple form, each atom would be replaced by a positive charge and the electrons by negative charges for the D-H bond, and the electrons by two negative charges for the lone pair of A. Knowing the geometry of the system, the bond eneray could be calculated by applying Coulomb's law, The values found in this way are close to ‘experimental values and the decrease in enery in passing from F to N, ic. with decreasing electronegativity, isalso well verified. However, there is no correlation. between thisenergy and thedipolemoment of A or D. Moreover, thedistance DA is, always smaller than the sum ofthe van der Waals radi, which indicates the exis ‘ence of forces other than electrostatic ones. “The quantum-mechanical treatment i difficult, but it brings out the fact that, in addition toan attractiveenergy of the Coulomb type, thereare three other forms of energy 1. The distance between the acceptor atom and H is less than the sum of the van der Waals radi (eg. the HO bond length in ge is 1.75 instead of 26), I follows that there must be a short-range repulsive energy 2, An attractive energy of the charge-transfer type (sce Box 2.4) is involved but the hydrogen bond is nota simple charge-transfer complex since inthis case it would require the quantity of charge transferred to inerease with the strength of the complex, which is not observed. 3. The polarizabilities of A and D lead to a dispersion (London) energy duc 10 the attractive coupling of the instantaneous dipoles produced by charge fuetuations, “The energies due to | and 2 are of the same order of magnitude as the electrostatic energy but, since they are opposite in sign, they will cancel cach other, and this explains why the electrostatic theory explains the hydrogen bond so well in some At the moment, there is no analytical form for the potential energy corres: ponding to the hydrogen bond, 262 Geometry and bifurcated bond ‘The hydrogen bond plays an essential role in explaining the physical properties of ‘water (see Part III) and in the binding of water molecules to biopolymers. Antibone orbitals Bonding In prote achelices, 4 and CO gn two hydro a| 2.6 THE HYDROGEN BOND Artbona orbitals ad Bonding orbitals Inproteins, we shall se that hydrogen bonds lock’ secondary structures such as, ‘ochelices, sheets and jturns. The majority of hydrogen bonds are between NH sand CO groups inthe peptide chain. The oxygen of CO ean, as in water, accept tivo hydrogens. A spatiel description of this bond (Fig. 2.6) requires three Figure2. Smpiiog dagram ola doner—accepir sytem ae 25 \@e.ut Figure 26 Spataparameters nthe pepade bond MOLECULAR BIOPHYSICS Parameters (1) the N-H-O angle, which isa measure ofthe linearity ofthe hydrogen bond: (2) the O-H distance, which is an indication of the bond energy: @) the C=O-H angle, or more precisely the angles 3 and >, which are a ‘measure of how far the three atoms deviate within the plane and out of it from the theoretically linear alignment of the C, O and H atoms, Forsmall molecules, theangle N-H—-Ois 16S" onaverageand theO—Hdistance is 1.87A. The latter distance may reach 1.95 A in proteins, with a higher mean deviation. The C=O-H angle has a mean value of 120° with values of 3 lying between Dand 40°. statistical survey ofa large number of proteins with structures known tohigh resolution has madeit possible toexamine morethan 1500 hydrogen bonds defined by H---0.< 2.4A and C=O:--H > 90°. Theresa tendency for the hydrogen bond to be oriented inthedirectionof the spsorbitalin thehydrogen atom. ‘Similarly, in nucleic acids, we shall see hydrogen bonds NH---N of O---HN being established between the complementary bases (A and T/U, G and C) and contributing to stabilization of double helices (type B, A or Z) and of some types, of triple helix. In the bond between water molecules and proteins or nucleic acid, a single ‘proton may be shared between two acceptor atoms (bifurcated bond) asin ‘The angle O-H—O is close to 90° but the two N-H-O angles are often unequal ‘The largest angle also corresponds to the shortest O-H distance and hence to the strongest bond, 2.63. Empirical analytical form for the potential In spite ofthe directional properties ofthe hydrogen bond, spherically symmetric potentials of the form r-!?— Br-'® are sometimes used. A form more in accordance with reality has recently been proposed: Bp = Seond-A'rst + Be )+ (1 —c0s6\(—arj* + Bri") (2.24) Where the angle @ is a measure of the non-linearity of the hydrogen bond (for ‘example, the angle N-H—O) and where the constants 4, B, A’, BY depend on the pairs of atoms involved ! | | | | ha single sanequal tothe tric jon the Calculation of conformations In determining the conformation of a macromolecular chain, calculating terms of, the form J;-J, leads only to a value for the mean distance (7) or the radius of ration. This is an inadequa ‘oncerned, proteins c description of the polymer, particularly where If we wish to be able to give accurate spatial coordinates for each atom, we must, use a set of interaction potentials beret * the valence bonds between bound atoms «the forces of attrac 3.1 Bound atoms 3.1.1 Valence bonds ion and repulsion between non-bonded atoms, ‘the atoms that takes into account Around the equilibrium value rp, we assume a harmonic potential of the following ‘ype Fos The values for K; in Table 3.1 are given by the AMBER program wi Kirn)? conformation calculations (Weiner eral, 1984). Similarly, around the equilibrium valence angle @ we assume a harmonic potential ofthe type: K3(0— 69)? an used in (2) and using AMBER once again, the typical values in Table 3.2 are found for Ky In practice, the values must be adjusted for each type of monomer by using those ‘obtained from small organic molecules whose structure is completely known, such as ethyl methyl ketone CH,-CO-28 MOLECULAR BIOPHYSICS ‘able 21 Values of Ky gen by the AMIBER program Bona ria (teamor AS) oe 1507 a7 1336 14g 1278 Table 2.2 Vates of Ks given by the AMBER program ange 1069) ‘Kelkcaimol rad) o-0-8 12 @ cnc wag 50 con m2 20 3.1.2 Torsional potential As we saw previously (eqn 1-12), we use an expression of the Following type for the potential energy due to rotation around the valence cone: Eps =(V/2)f1 +e08(06 — 9] (3) For example, X-C-C-X has n = 3.7 =Oand V/2~2kealmol *. giving poten- tial barriers of about 4 kcal mol’, The interactions involvedin the rotation around the valence bond are mainly those between atoms bonded for example to two ‘carbons, and those of electron orbitals surrounding the two carbons. 3.2 Non-bonded atoms We saw previously that all the interactions between atoms or groups of atoms fell into three distinet groups: Coulomb interactions, interaction of the London—van der Waals type and hydrogen bonds. ‘The form taken by the potential energy has been determined for each group (soe ‘Table 2.1), so that overall the total interaction energy has the Following general Form summed over all atoms: Be =D Kiley + KOA)? + (PDI —coskns vw + Daler + Dldu/e— By/4 + (che*— vir) (34) and this s the basis of the AMBER program, Several difficulties remain L. In Coulomb-type interactions, which are all the greater in that they obey the Tong-range I/r law, it is not easy to choose values for qi, g2 and ©. A screening effect due to both the dielectric constant of water and the presence of free ions sometimes leads to a considerable reduction in the energy: A similar effect occurs in the presence of ion pairs that reduce the net charge 4. 3. The choice of a value for « is made difficult because ofthe large variation in dielectric constant near a charge (see section 16,2.2 and Chapter 19), 3.3 Tor Covalent b involved i disulphide position in A bond lik in maintai phosphod closed cre 3.4 Hel conformat experiment ‘macromok A frequx described axis whilet character next by rt axis. The rotation (a Morepn bythefollo ofthe heli where ris) depending The rat bby he sens is right-ha positive usual igo The sens viewed!) handed ser In prote play a role motif) and3.3 TOPOLOGICAL CONSTRAINTS 3.3 Topological constraints ‘Covalent bonds between atoms a long way from each other along a chain can be involved in the building of three-dimensional structures. Examples inelude the disulphide bridges created in proteins by the oxidation of two SH groups whose Position inthe chain i indicated by the symbol > SSH SH-< +4 S—< + A bond like this isnot included in the previous calculations, but it plays a key role in maintaining a well-defined structure. Another example is provided by the phosphodiester bonds established between the two ends of a DNA chain to ereate 1, then the minus sign is appropriate and 2; =, so that dnjds=1 and (3.17) _G18) than 1. (G.17) (3.170) 3.5 THE HELIX-COIL CONFORMATIONAL TRANSITION 3536 Figure 31 Farsiton curves tor varous values of MOLECULAR BIOPHYSICS 10 005 zpos 2 5 ‘s(logarithmic scale) ‘Once again, we have the ‘all or nothing’ phenomenon already examined, which corresponds to a phase transition in the thermodynamic sense. The curves for ‘s) in Fig, 3.1 illustrate the general form of the transition, The slope at the brigin (5= 0, @= 0) iso. Only the curves for ¢ < I have a point of inflection for s=1 and @=1/2. ‘A transition width can be defined by As = (d8/ds),4, (3.18) (in Fig. 32, As= AA‘+BB)), Differentiating 0 with respect tos gives (Fig. 3.2): days = (1/A1) Ai fds — (5/9) / ds} + (9/1) Pr /s® G19) We only have to calculate dy (ds? and replace sby 1 in this, to give 6/85 = (1-4 0! + 0) /4(0 + al!) = 1/(4e! (320) ae (since = ‘The width the nucleati have from: constant: The tran and since d8 sincefors = ‘passing from is an appars process. Itsy directly by3.5. THE HELIX-COIL CONFORMATIONAL TRANSITION. (since #10) and hence Asada! @2n The width ofthe transition is therefore a direct measure ofthe cooperativity. i.e the nucleation parameter. When the transition iscaused by a rise in temperature, we have from the definition of s (s=exp(—AG/RT)) similar to an equilibrium dinsy/a Any RT (a2) ‘The transition width AT is defined inthe same way as before by AT =(d0/dT)"', and since d@/a7 = (40 dsyds'47), we obtain AT =4o!?RT2/AH (3.23) sincefors = 1, P= Ty (the transition temperature), Ais thechangeinenthalpyin passing from thehelixto the oil. should be pointed out that in thisexpression A is an apparent enthalpy, which takes account of the cooperative nature of the process. Is value may be completely diferent from the changein enthalpy obtained directly by calorimetric measurements, 7 ° Figure 3.2 Curve ordstnton of srenetion with 2