the protein may exist in one conformation in the absence of ligand the ligand that binds. On the contrary, the binding of different
|
|
- Ann O’Neal’
- 5 years ago
- Views:
Transcription
1 Proc. NatL Acad. Sci. USA Vol. 80, pp , January 1983 Biochemistry Alternate model for the cooperative equilibrium binding of myosin subfragment-l-nucleotide complex to actin-troponin-tropomyosin (muscle contraction/regulation/calcium/ising model/matrix method) TERRELL L. HILL*, EVAN EISENBERGt, AND LOIS E. GREENEt *Laboratory of Molecular Biology, National Institute of Arthritis, Diabetes, and Digestive and Kidney Diseases, and tlaboratory of Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland Contributed by Terrell L. Hill, October 4, 1982 ABSTRACT In this paper we introduce an alternate model for the equilibrium binding of S-i-N (S-1, subfragment 1 of myosin; N. nucleotide) on the troponintropomyosin--actin complex, including the influence of Ca2+ on this binding. In our previous model [Hill, T. L., Eisenberg, E. & Greene, L. E. (1980) Proc. NatL Acai Sci USA 77, ], we assumed that each tropomyosin unit, including one troponin-tropomyosin molecule and seven actin sites on the actin filament, could exist in two conformational states which presumably differed in the position of the tropomyosin on the actin. The binding of S-i-N or Ca2+ to the tropomyosin unit shifted the equilibrium between the two states but did not affect the intrinsic conformation of each state. In contrast, in the present model, we assume that tropomyosin can in principle occupy a continuum of positions on the actin filament. However, in any particular circumstance (N, Ca2+, salt, temperature), the tropomyosin occupies only a single position rather than existing in a dynamic equilibrium between two positions as in our earlier model. The binding of S-i-N or Ca2+ changes the position of tropomyosin on the actin filament and the exact position that the tropomyosin occupies depends on the nucleotide bound to S-1. In an earlier paper (1) we introduced a model for the cooperative equilibrium binding of myosin subfragment 1 (S-1) to the troponin-tropomyosin-actin complex (regulated actin). In this model, the tropomyosin units, consisting of seven actin sites and one troponin-tropomyosin molecule, exist in two conformational states: state 1, in which actin binds S-1 wealdy, and state 2, in which actin binds S-1 strongly. Presumably, the tropomyosin molecule occupies a different position on the F-actin filament in each of these states; intermediate positions (or states) are assumed not to occur. One of the key properties of this model is that, under all conditions, there is an equilibrium between the two structural states of the tropomyosin units; the binding of Ca2O or S-1 to the tropomyosin units shifts the equilibrium between the two states but does not affect the intrinsic conformation of each state. This model can account for the interaction of regulated actin with S-1, S-1PADP, S-l adenosine 5'-[,Sy-imido]triphosphate (S-1'AMP-P[NH]P), and S-1FATP (2, 3), although it is necessary to assume that the ratio of S-1 binding affinity to the strong and weak states (i.e., K2/K1) of the tropomyosin units depends on the nucleotide bound to S-1. This ratio is quite high with S-1 and S-1 ADP, whereas it is almost 1 with S-1 ATP. As we have discussed elsewhere (4), the interaction of a protein and a ligand can occur in a somewhat different manner. Rather than the protein existing in two intrinsically stable conformations, independent of the presence or absence of ligand, The publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C solely to indicate this fact. 60 the protein may exist in one conformation in the absence of ligand and then, when ligand binds, be induced to enter a quite different conformation. In this well-known type of "induced fit" model, the conformation of the protein is not independent of the ligand that binds. On the contrary, the binding of different ligands-e.g., S-1PADP and S-1 AMP-P[NH]P--could induce somewhat different conformations. In the present paper we apply this approach to the cooperative equilibrium binding of S-1 to regulated actin by allowing the tropomyosin to occur in a continuum of positions on the actin filament. In a way, this new induced fit model is as simple as our "two-conformation" model. Although the tropomyosin can exist in a continuum of positions, this model has the simplicity that under any particular circumstance (N, Ca2+, salt, temperature), the tropomyosin can occur in only one position rather than in two positions, as in our earlier model. The new induced fit model is able to fit our experimental data as well as our earlier two-conformation model, although to fit our data it is necessary to assume that the position into which the tropomyosin is "pushed" depends on the nucleotide bound to S-1. This is analogous to the requirement in our earlier model that the ratio of S-1 binding strength to the two states of the tropomyosin units depends on the nucleotide bound to S-1. THE ASSUMED MODEL In the absence of Ca2', we assume that the tropomyosin-troponin complex can exist in two different states, labeled 10 and 2 in Fig. 1. Each tropomyosin-troponin complex covers seven actin sites for the binding of S-1-N (N, nucleotide). If no S-1- N is bound to a seven-site tropomyosin-troponin-actin unit, then the tropomyosin-troponin is in state 1 The tropomyosintroponin complex in this state blocks the access of S-i-N to the actin sites. In order for an S-1-N to be able to bind to an actin site, the S-1-N must, as part of the binding process, push the entire tropomyosin-troponin complex to a new position or state, relative to actin, labeled 2 in Fig. 1. The figure is, of course, schematic. The positive free energy required to move the tropomyosin-troponin is denoted AG. It is assumed that the location of state 2 relative to state 10 and the value of AG could be different when different nucleotides (or no nucleotide) are attached to S-1, because the bound nucleotide may affect the angle at which S-1 binds to actin. Thus, state 2 is not an intrinsic second location for tropomyosin-troponin but rather a location forced on tropomyosin-troponin by the binding of S-1-N. Fig. 1 represents, schematically, the position of tropomyosin in states 10 and 2, as well as in states 1I and III. As discussed below, state 1 is divided into the three states 10, I1, and 1II, depending on the number of Ca2' bound to troponin C. Fig. 1 Abbreviations: S-1, myosin subfragment 1; S-1iAMP-P[NH]P, S- ladenosine 5'-[13,y-imido]triphosphate.
2 Biochemistry: BProc. Hill et al Natl. Acad. Sci. USA 80 (1983) 61 Tm Tn Tn+Ca2+ Tn+2Ca2+ OLD State 1o 11 II i 2 Actin Sits S-1- FIG. 1. Schematic representation of four. states of tropomyosintroponin in model. Troponin undergoes a conformational change (circle,square, rectangle) when Ca2" is bound (heavypoint), causingtropomyosin-troponin (Tm-Tn) to change position in relation to the actin sites when tropomyosin-troponin is in state 1 (substates 10, 1i, III, according to number of Ca2+ bound). When S-1-N is bound, tropomyosin-troponin is in state 2, with a position relative to actin sites that is independent of troponin conformation. can alternatively represent the relative free energies of the four states in these positions. After the first S-1-N is bound to a unit, subsequent S-1-Ns can be bound without any further movement of or free energy expenditure on the tropomyosin-troponin complex. If the subsequent S-1-Ns bind with binding constant K2, then the binding constant of-the initial S-1-N to a unit is e-g/ktk2, or K2/L, if we define L as eag'it. k Thus L 1. When, as usual, L > 1, the binding of the first S-1-N to a unit is inhibited by the extra work that has to be done to move the tropomyosin-troponin. In general, both K2 and L-will depend on N. In our previous model (1), an independent parameter K1 (not needed here) was the "early" binding constant (here it is K2/L). In our earlier model (1) we postulated that, with no S-1-N bound, a dynamic equilibrium exists between tropomyosin-troponin in two different states 1 and 2, with equilibrium constant L. This L is necessarily independent of N; it is an intrinsic property of the actin filament. Here there is no such dynamic equilibrium. Instead, with no S-1-N bound, tropomyosin-troponin is in state 10; with one or more S-1-N bound, tropomyosin-troponin is in state 2. Thus, the state change is part of the binding process. L in the present model depends on N because the state 2 position of tropomyosin-troponin, established by the binding of S-1-N, is generally different for different N. Fig. 2 shows very schematically the physical origin of the difference between the binding constants K2/L and K2. In the former case, work has to be done separating tropomyosin-troponin from the row of actin sites, but this is not so in the latter case. Incidentally, if K' (Fig. 2) is the binding constant for S-1- N on actin in the absence of tropomyosin-troponin, we would expect K2 > KS if there is an attractive interaction between tropomyosin-troponin and S-1-N (Fig. 2). A small effect of this sort is observed (2, 3): k/k2 3 when N = ADP or AMP-P[NH]P. In this model, as previously (1), we assume that there are no direct interactions between neighboring bound S-1-N molecules. This assumption is based on the observed independent binding of S-1 ADP on actin in the absence of tropomyosintroponin (2). The assumption, above, that a single S-1-N bound on any of the seven sites of a unit will move the entire tropomyosin-troponin into a new state, state 2, has been relaxed in ref. 5. If we call the present case R = 7, where R is the number of actin sites undergoing the 10 -> 2 state change when an S-1-N is bound to one of the two end sites of a tropomyosin-troponin unit, then it can be shown (5) that R = 6 and R = 5 are also possible choices for a model, but not R 4. In the absence of structural or other - information to the contrary, we are adopting the R = 7 model here for mathematical simplicity. Perhaps tropomyosin, a twochain a-helical coiled -coil (6), is sufficiently rigid to indicate R = 7 i any case. We have found experimentally (2, 3) that, if tropomyosintroponin is saturated with Ca2", the value of L decreases while. K2/L: e'i + K2: (s) + K0: (s) + Tm Tmfi - SXi Afi lb S- Tm' FIG. 2. Schematic relation between binding constants of S-1-N. K2/L: The first S-1-N bound to a tropomyosin-troponin-actin unit must move tropomyosin-troponin relative to actin, as part of the binding process. K2: Subsequent S-1-N molecules bind to the unit without havingto move tropomyosin-troponin. K02: Bindingof 5-1-N to unregulated actin occurs without interaction between S-1-N and tropomyosintroponin. See text. Tm, tropomyosin. K2 is not significantly affected. These facts are reflected in our model by assuming (Fig. 1) that when no S-i-N is bound (state 1), binding of Ca2+ on troponin also moves tropomyosin-troponin relative to the actin sites, possibly through a conformational change in troponin; but when S-1-N is bound (state 2), the binding of Ca2" has no effect on the state 2 position of tropomyosin-troponin relative to the actin sites. Thus, if we include the possibility of Ca2" binding, state 1 is subdivided into three states, 10, 1I, 1i (Fig. 1), the second index (0, I, or II) referring to the number of Ca2" bound-on the two regulatory sites of troponin. Fig. 1 is very schematic; it is meant to indicate that the free energy AG necessary to move tropomyosin-troponin from state 1 into state 2, to accommodate S-1-N binding, is decreased when two Ca2" ions are bound on troponin (state III) as compared to the case (discussed above) in which Ca2" is absent (state 10). So to speak, state III has a head start over state 10 in the direction of state 2 (state 11 is intermediate). Consequently, L is smaller at high Ca2" than at low Ca2+ concentration. We assume that the more extensive movement of tropomyosin-troponin relative to actin, induced by S-1-N binding, supersedes any Ca2` effect on the position of tropomyosin-troponin. Thus, state 2 is not altered in position and K2 is not affected by Ca2+ binding. Strong cooperative binding of S-1-N on regulated actin is observed in some cases (2, 3). To account for this, we have assumed previously (1), and continue to do so here, that there are nearest-neighbor interactions between the ends of units-that is, between the ends of tropomyosin molecules (7). This is referred to as the tropomyosin-tropomyosin interaction below. These tropomyosin ends are, in fact, known to be in contact one way or another (6). We assume here that the optimal interaction between two ends occurs when both tropomyosin molecules are at the same position (i.e., state) relative to the actin sites and that the greater the difference in position (Fig. 1) of the two molecules (or states) the more the optimal interaction between the ends is decreased. For the four possible states in Fig. 1, there are 10 possible kinds of nearest-neighbor pairs, which we denote by (using the second state 1 index): 00, 01, OII, 02, I I, III, 12, II II, 112,.and 22. Some examples are shown in Fig. 3. This is schematic. Contact between ends is not shown in the figure but it is presumably always present, though with some
3 62 Biochemistry: Hill et al, Proc. Natl. Acad. Sci. USA 80 (1983) Tm-Tn Pair 00 OIl State , 2 2 Actin S-1-N FIG. 3. Notation used to designate the four states and the 10 kinds of nearest-neighbor pairs in the model. See text. distortion when the two molecules are in different states. If, for any one of these pairs, wi1 is the free energy of interaction of the two ends relative to their infinite separation, then we define X - ewkt. We can simplify notation for all of the like pairs, with optimal interaction (see above), by using a single x: X = Xoo = XI I = XII II=X22. [1] In view of the comments above, xi, = xji and we have, for example, the inequalities: X22 = X x112 2 Xx12 X02, [2] Xoo = X X- x01 X01 X02- In both lines, the separation. (Fig. 1) between the two states increases as we move to thetight. An equality would occur only if the levels (Fig. 1) of the two states were the same, in a special case. As will be seen below, these inequalities describe qualitatively the dependence of the tropomyosin-tropomyosin interaction parameter Y (1) on nucleotide and on Ca + that is predicted by the present model. FORMULATION AND PROPERTIES OF THE MODEL We can use the matrix method, as before (1, 5), to deduce the exact properties of the nearest-neighbor Ising model outlined above. Because there are four states (Fig. 1), we have to start with a 4 x 4 matrix. The grand partition functions for the four states are: 10: 1 11: 2Kap 111: aka:p2 2: L-'[(1 + K2c)7-1](1 +-2Kbp + fk2bp2)-2&. the concentration of Ca2", c is the concentration of Here p is S-1-N, Ka is the binding constant of the first Ca2+ on state 1 (the factor of 2 for 11 implies the assumption of two equivalent binding sites), aka is the-binding constant of the second Ca2+ on state 1, and Kb and /3 are similar for the state 2 binding of Ca2+. In 2- L-1 [ ] (Eq. 3), unity is subtracted within because state 2, by definition, never has all actin sites empty (state 1 takes care of this case). The factor L' multiplies each of the remaining terms in [ ] because L is involved (in K2/L) only for the first S-1-N bound, but not in any subsequent binding. The binding constant Ka (in 1I) includes any contributions from a troponin conformational change and from forced movement of tropomyosin-troponin from position 10 to 1I (Fig. 1). Thus, Ka for Ca2+ is analogous to K2/L-for S-1-N. The factor a takes care of any possible difference in free energy required, for a troponin conformational change and for tropomyosin-troponin movement, between 10 -o 1I and I11; a also takes care of Ca2+-Ca2+ repulsion (in HI), if any. The factors f2 and (Eq. 3) are independent (can be simply multiplied) because Ca2+ binding in state 2 is assumed not to perturb the position of tropomyosin-troponin (as it does in state 1). Therefore, Kb does not have a contribution from tropomyosin-troponin movement (as Ka does), and 8 is related only to the troponin conformational change (as in a) and to possible Ca2+-Ca'- repulsion. If the second Ca2+ is bound with more difficulty than the first (negative cooperativity), a, ( < 1. We would expect from the above discussion that Ka < Kb, but whether a < 83 or (3 < a depends on the free energy differences between states 10, 11, and 111 for tropomyosin-troponin. The 4 X 4 matrix (1, 5), including nearest-neighbor interactions, is x 2KapxoI akap2x0j1 i XoI 2Kapx ak~p~xju ~AXKp 12 XO{I 2K'aPXIII akap x (24XI12 X02 2KaPXI2 aknp XI12 24X v 24X02 Even with simplifying assumptions about regularity in the x., the largest eigenvalue y)m (m means maximum) of this matrix has to be found by solving numerically (5) a quartic equation in y. The binding isotherms for S-1-N and Ca2+ then can be calculated, numerically, from (1, 5) 70 = aln ymalnc and o- = aln ym/alnp, [5] respectively, where 0 0 S 1 (for S-1-N) and o- 2 (for - Ca2+). Actually, experiments at intermediate p (Ca2+ concentration) are not available yet. The important special cases, for comparison with experiment, are p- 0 and pa- oo. In the former case, only states 10 and 2 (with 4X, = 1) are important. Thus, we have a 2 X 2 matrix: / x X02 X [6]- VL-1[ ]0 L-'[,JI o) where [ ] appears in Eq. 3. In the latter case (p-k oo), only states OII and 2 (with 4, = 3Kbp2) are significant. The 2 X 2 matrix is 1 akap x akpz X112 [7] 3KJp%4.XII2 OKbO x If, to normalize, we divide each element of this matrix by ak'p2 (this will not affect Eq. 5 for 0), we have x X112 [3] (P [8] ), where Thus L(oo), defined here, has the same significance for p -> 00 that L does for p -a Because we expect Ka < Kb (free energy is required to move tropomyosin-troponin when Ca2" is bound in state 1), presumably L > L(oo), as is observed experimentally (1, 3). As a numerical example, on fitting the two Ca2+ binding curves in Fig. 2 ofref. 8 using f (S-1 present) and the equivalent (a (S-I absent), we find Ka = 3.6 X 106 M-l, Kb = 9.5 X 106 M-l, a 15, = = 4 [10] These values predict, from Eq. 9 that L = 18.6 L(oo) for S-i binding (note, however, that the experimental curves refer to all four Ca2" sites on troponin, not just the two regulatory sites). Kb, a,. and A will not generally be available to allow application of Eq. 9. The usual procedure will be to find L and L(oo) independently by curve fitting of S-1-N binding data, in the absence and in the presence of Ca2+. But we can anticipate, from Eq. 9, that L 3 L(oo). Reliable values of K&, L(oo)-'[ IX,,2 L(oo)-'[ ]x = L(oo) L(aKa 2/pK2b). Eqs. 8 and.6 have the same form except that L(oo) replaces L and x112 replaces x02. We define nearest-neighbor interaction [4] [9]
4 Biochemistry: parameters (1, 5) Hill et al Y(oo) = (X/X112)2, Y = (XIX02), [11] where Y(oo) applies when p -+00 and Y applies when p -+ Because state 11I is nearer to state 2 (Fig. 1) than is state 10 (on account of Ca2+ binding in the former case), x112 > x02 (Eq. 2) and Y > Y(oo). It is not possible to determine experimentally whether Y > Y(oo) because the slight cooperativity observed in the presence of Ca2+ makes the data very insensitive to Y(oo) (3) Ȧccording to our model and assumptions, the greater the separation in position and free energy between states 10 and 2 (Fig. 1), the larger the value of L and the smaller the value of x02 (Eq. 2). If the nucleotide N is changed, in S-1-N, state 10 is unaffected but the position of state 2 may be higher or lower (e.g., because of a change in binding angle of S-1-N). For example, if state 2 is higher, L increases and xo decreases. The value of x is unaffected (it is the optimal interaction parameter for neighboring tropomyosin ends when the two tropomyosin molecules are at the same level-that is, in the same state). Thus, in this example, in view of Eq. 11, Y increases as well as L. In general, when either N or Ca2+ (present or absent) is changed, the values of L and Y are expected to go up or down together. The following analysis is based on Eq. 6, using L and Y (p -+ 0). But, in the presence of Ca2' (p-+ oo), the-same equations are applicable if we merely replace L and Y by L(oo) and Y(oo). The other parameter, K2, is not affected by Ca2'. The larger eigenvalue Ym of Eq. 6 is given by 2ym = a, + a2 + [(a, - a2)2 + 4al42y-l]"l2, [12] where a, = x and a2 = xl-'[ ]. The fraction 6 of actin sites occupied by S-1-N molecules then is found from Eq. 5 to be 6 = P202, [13] where 62 = K2c(1 + K2c)6/[(1 + K2c)7-1] [14] P2 = 2aY-/'f(l - a + V) [15] a-a2/a, = f2 = L'[(1 + K2c)7-1] [16] [(1 - a)2 + 4aY-']1/2. Here, P2 is the fraction of units in state 2, 62 is the fraction of state 2 actin sites that are occupied by S-1-N, and a is the equilibrium constant, per unit, for the transition 10 -± 2 between a filament with all units in state 10 and a filament with all units in state 2 (the interaction parameter is x in both cases and cancels). The transition (as c increases) is half-completed (P2 = 1/2) when a = 1. Note that a does not depend on Y; but the steepness of the transition at a = I (P2 = 1/2) increases with Y. The above results resemble those in ref. 1, but there are significant differences. Here 61 = 0 (no binding on state 10 units) and 62 is not a simple Langmuir binding isotherm [except when K2c>> 1, in which case K2c/(1 + K2c)]. In fact, when K2c - 0, 62-> 1/7 (a state 2 unit necessarily has at least one S-1- N bound). The equilibrium constant a has a correspondingly different form than in ref. 1. Also, Y and L have more explicit physical interpretations here. In particular, L is related to the alteration of the tropomyosin-troponin position on binding the first S-1-N to a unit; L is not an isomeric equilibrium constant as in ref. 1. Incidentally, adsorption with perturbation of the absorbent by the adsorbate, as in the present model, is a common-phenomenon (9). Proc. Natl. Acad. Sci. USA 80 (1983) 63 When K2c -> 0, /7, a-- 7K2c/L, P2 a/y, 6-- K2c/LY. [17] Thus, the initial slope of O(c) is K2/LY. This is the effective binding constant in the initial binding of S-1-N. Y appears in this last expression because each new S-i-N bound on a chain of units practically devoid of bound S-i-N will convert a state 10 unit into a state 2 unit (binding constant K2/L) and, at the same time, transform two-00 neighbor interactions (parameter x) into two less favorable 02 interactions (parameter x02). When Y = 1 (no interaction effects), P2 = a/(l + a). The binding isotherm 6(e) still shows positive cooperativity in this case, if L >> 1, because of the groups of seven sites switching state (10 -+2) as a unit. When L>> 1, there is strong inhibition of early binding (K2/L) followed by relatively easy binding (K2) on state 2 units. When L = 1 as~well as Y = 1, Eq. 13 reduces to simple Langmuir binding: 6 = K2c/(l + kc), with no cooperativity at all. Evaluation of Parameters. The usual procedure in evaluating parameters, given a set of experimental O(c) data, is the following: (i) From each of the high c points (usually 6> 5), K2 is calculated by using K2 = 6/(1-6)c (or, if necessary, Eq. 14) and then is averaged. (ii) By using this (averaged) K2, the curve 02(c) (Eq. 14) is calculated and drawn. This curve should be a good representation of the high c points. (iii) A smooth curve O(c) is drawn through the experimental data in the (inflection) region that includes the point where 6 (experimental) = 02/ 2. The values of 6 and c where 6 = 62/2 are denoted 6' and c' (see Fig. 4). This is the point at which P2 = 1/2 (Eq. 13) and a = 1. (iv) The value of L may now be calculated from Eq. 16: L= (1 + K2c')7-1. [18] There is a corresponding, but not independent, connection between 6' and L: 6' = [(L + 1)/7 -_1](L + 1)6'7/2L. [19] (v) The full theoretical curve. 6(c) is calculated now from Eq. 13 (by using K2 and L found above), adjusting Y for best fit [especially to match the observed slope in 6(c) in the neighborhood of c = c']. (vi) Because there is some flexibility in drawing the smooth curve in step iii, -above, the overall agreement between the theoretical and experimental 6(c) can sometimes be improvedbyadjusting 6' and c' slightly, consistentwith 6' = 02(c')/ 2. Fig. 4, which examines the binding of both S-1ADP and S- 1AMP-P[NH]P to regulated actin -under identical conditions (the absence of Ca2+,,- = 18 M, 25 C), illustrates the above procedure. These data have been analyzed previously by using our original model (3). For the AMP binding data (Fig. 4A), the parameters that give the solid theoretical line with our new model are K2 =-1.46 X 10J M-1, c' 52,uM, 6' = 22, L = 51.1, and Y = 2 Stnilar parameters were obtained when we fitted these data with our old model (3). In applying our new model to the AMP-P[NH]P data, we could not get a.very good fit to the data employing the same values for L and Y- that we used above for the ADP data (dashed line in Fig. 4B). However, by decreasing the values of both L and Y, we were able to obtain a much better fit. -The solid theoretical line for the AMP-P[NH]P data (Fig. 4B) was obtained with the parameters- K2 = 1.27 X 104 M-1, c' = 50,uM, O' - 20, L-= 32, and Y-= 4. Note that these same values of L and Y give a poor fit-to the ADP data (dashed line in Fig. 4A). Thus, to account for our data with the new model, it is necessary to assume that S-1.AMP-P[NH]P does not push the tropomyosin to quite the same position on the actin as does S-1 ADP;
5 n A Kn Biochemistry: Hill et'al.,,.6 0 0~~~~ 45 - o / / 0 / C, /M FIG. 4. Fitting of the model to data obtained for the binding of S- 1'ADP and S-1 AMP-P[NH]P to regulated actin in the absence of calcium (,u = 18 M, 250C). (A) For the ADP data, the solid theoretical line was obtained by using K2 = 1.46 x 106 M-1, L = 51.1, and Y = 2 The dashed line was obtained with the same value of K2 and L = 32 and Y = 4. (B) For the AMP-P[NH]P data, the solid theoretical line was obtained by using K2 = 1.27 x 104 M-1, L = 32, and Y = 4. The dashed line was obtained with the same value of K2 and L = 51.1andY= 2 the binding of S-1-ADP requires a larger change in the position of the tropomyosin than does the binding of S-1.AMP-P[NH]P. This might occur if S-1-AMP-P[NH]P binds to actin at a somewhat different angle than does S-1-ADP (10-12). DISCUSSION In this paper we have presented a new cooperative model that accounts for our binding data as well as does the old model. The major difference between the two models lies in the nature of J Proc. Natl' Acad.- Sci. USA 8a (1983) the states of the tropomyosin. units of regulated actin. In the old model, no matter what the conditions, there are only two intrinsic states for each of the units, states 1 (weak binding) and 2 (strong binding). The binding of Ca2' or S-i affects the equilibrium between-the two states. In addition, the S-i binding constants K1 and. K2, to units in states 1 and 2, are different for different.s-l-nucleotide complexes, which also affects the 1 a± 2 equilibrium.. Thus, the lack of a cooperative effect with S-1FATP is attributed, in this model, to nearly identical binding of S-FATP to states 1 and 2 (K1 -K2). In contrast, in the new model, a tropomyosin molecule is, in principle, able to occupy a continuum of positions (relative to the groove) on the. F-actin filament. The binding of Ca2+ shifts the position of the tropomyosin molecule as does the binding of S-i. In the latter case, the position to which the tropomyosin is shifted depends on the nucleotide bound to S-i. Thus, with the new model, the lack of a cooperative effect with S- 1ATP would be attributed to the ability of an S-1ATP to bind. to actin without causing any significant change in the position of the corresponding tropomyosin molecule on the F-actin filament. It may be possible to distinguish between the two models experimentally. A fluorescence change occurs when S-i or Ca2' binds to regulated actin. If a tropomyosin molecule can occupy a continuum of positions on the F-actin filament, then the magnitude of this fluorescence change might depend on.the position of the tropomyosin on the F-actin filament, which, in turn, could be affected by the nucleotide bound to the S-i. IfS-1ADP and S-1AMP-P[NH]P push the tropomyosin to different positions, the cooperativity observed in the regulated actin S- 1ATPase activity also might be different, depending on whether ADP or AMP-P[NH]P is present in addition to ATP. These experimental approaches must be. explored to distinguish between our original model and the model presented in this paper. 1. Hill, T. L., Eisenberg, E. & Greene, L. E. (1980) Proc. NatL Acad. Sci. USA 77, Greene, L. E. & Eisenberg, E. (1980) Proc. Nati Acad. Sci. USA 77, Greene, L. E. (1982) J. Biol Chem., in press. 4. Hill, T. L. & Eisenberg, E. (1981) Q. Rev. Biophys. 14, Hill, T. L. (1981) Biophys. Chem. 14, Phillips, G. N., Fillers, J. P. & Cohen, C. (1980) Biophys. J. 32, Wegner, A. (1979)J. MoL BioL 131, Bremel, R. D. & Weber, A. (1972) Nature (London) New BioL 238, Hill, T. L. (1950)J. Chem. Phys. 18, Marston, S. B., Rodger, C. D. & Tregear, R. T. (1976) 1. Mol. BioL 104, Chalovich, J. M., Greene, L. E. & Eisenberg, E. (1982) Biophys. J. 37, 263a (abstr.). 12. Eisenberg, E. & Greene, L. E. (1980) Annu. Rev. PhysioL 42,
Adsorption from a one-dimensional lattice gas and the Brunauer Emmett Teller equation
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 1438 1433, December 1996 Chemistry Adsorption from a one-dimensional lattice gas and the Brunauer Emmett Teller equation (Ising modelreference systemgibbs ecess
More informationMuscle regulation and Actin Topics: Tropomyosin and Troponin, Actin Assembly, Actin-dependent Movement
1 Muscle regulation and Actin Topics: Tropomyosin and Troponin, Actin Assembly, Actin-dependent Movement In the last lecture, we saw that a repeating alternation between chemical (ATP hydrolysis) and vectorial
More informationA Model Based Analysis of Steady-State versus Dynamic Elements in the Relationship between Calcium and Force
A Model Based Analysis of Steady-State versus Dynamic Elements in the Relationship between Calcium and Force Casey L. Overby, Sanjeev G. Shroff BACKGROUND Cardiac contraction and calcium. Intracellular
More informationRegulation of the Interaction between Actin and Myosin Subfragment 1: Evidence for Three States of the Thin Filament
Biophysical Journal Volume 65 August 1993 693-71 Regulation of the Interaction between Actin and Myosin Subfragment 1: Evidence for Three States of the Thin Filament 693 Daniel F. A. McKillop* and Michael
More informationto the three terminal subunits of the filament that form the The helical actin filament is illustrated schematically in Fig.
Proc. Natl. Acad. Sci. USA Vol. 82, pp. 727-7211, November 1985 Biochemistry A model for actin polymeriation and the kinetic effects of ATP hydrolysis (ATP cap/steady state/cap-bdy interface) DOMINIQUE
More informationLecture 13, 05 October 2004 Chapter 10, Muscle. Vertebrate Physiology ECOL 437 University of Arizona Fall instr: Kevin Bonine t.a.
Lecture 13, 05 October 2004 Chapter 10, Muscle Vertebrate Physiology ECOL 437 University of Arizona Fall 2004 instr: Kevin Bonine t.a.: Nate Swenson Vertebrate Physiology 437 18 1. Muscle A. Sarcomere
More informationCa 21 and Ionic Strength Dependencies of S1-ADP Binding to Actin-Tropomyosin-Troponin: Regulatory Implications
Biophysical Journal Volume 87 September 2004 1825 1835 1825 Ca 21 and Ionic Strength Dependencies of S1-ADP Binding to Actin-Tropomyosin-Troponin: Regulatory Implications Boris Gafurov, y Yi-Der Chen,*
More informationAccording to the diagram, which of the following is NOT true?
Instructions: Review Chapter 44 on muscular-skeletal systems and locomotion, and then complete the following Blackboard activity. This activity will introduce topics that will be covered in the next few
More informationcycle of the isometrically contracting state); bridges; and in both cases, there was an additional
THE JOURNAL OF BIOLOGICAL CHEMlSTRY 0 1987 by The American Society for Biochemistq ' and Molecular Biology, Inc Vol. 262, No.28, Issue of October 5, PP. 13627-13635,1987 Printed in U. S. A. Effect of Rigor
More informationBMB Lecture 7. Allostery and Cooperativity
BMB 178 2017 Lecture 7 October 18, 2017 Allostery and Cooperativity A means for exquisite control Allostery: the basis of enzymatic control From the Greek: allos = other stereos = solid or space Action
More informationTheoretical study of the effect of enzyme-enzyme interactions
Proc. Natl. Acad. Sci. USA Vol. 74, No. 9, pp. 3632-3636, September 1977 Chemistry Theoretical study of the effect of enzyme-enzyme interactions on steady-state enzyme kinetics (enzyme lattice/enzyme solution/ising
More informationCooperative Regulation of Myosin-Actin Interactions by a Continuous Flexible Chain II: Actin-Tropomyosin-Troponin and Regulation by Calcium
3168 Biophysical Journal Volume 84 May 2003 3168 3180 Cooperative Regulation of Myosin-Actin Interactions by a Continuous Flexible Chain II: Actin-Tropomyosin-Troponin and Regulation by Calcium D. A. Smith
More informationBMB Lecture 7. Allostery and Cooperativity. A means for exquisite control
BMB 178 2018 Lecture 7 Allostery and Cooperativity A means for exquisite control Allostery: the basis of enzymatic control From the Greek: allos = other stereos = solid or space Action at a distance Examples
More informationTransport of single molecules along the periodic parallel lattices with coupling
THE JOURNAL OF CHEMICAL PHYSICS 124 204901 2006 Transport of single molecules along the periodic parallel lattices with coupling Evgeny B. Stukalin The James Franck Institute The University of Chicago
More informationIntroduction: actin and myosin
Introduction: actin and myosin Actin Myosin Myosin V and actin 375 residues Found in all eukaryotes Polymeric Forms track for myosin Many other cellular functions 36 nm pseudo-helical repeat Catalytic
More informationSupporting Text Z = 2Γ 2+ + Γ + Γ [1]
Supporting Text RNA folding experiments are typically carried out in a solution containing a mixture of monovalent and divalent ions, usually MgCl 2 and NaCl or KCl. All three species of ions, Mg, M +
More informationStructural determinants of cooperativity in acto-myosin interactions
Vol. 49 No. 4/2002 805 812 QUARTERLY Rewiev Structural determinants of cooperativity in acto-myosin interactions Joanna Moraczewska Kazimierz Wielki University of Bydgoszcz, Institute of Biology and Environmental
More informationAn Introduction to Metabolism
An Introduction to Metabolism I. All of an organism=s chemical reactions taken together is called metabolism. A. Metabolic pathways begin with a specific molecule, which is then altered in a series of
More informationLecture 7: Simple genetic circuits I
Lecture 7: Simple genetic circuits I Paul C Bressloff (Fall 2018) 7.1 Transcription and translation In Fig. 20 we show the two main stages in the expression of a single gene according to the central dogma.
More informationSKELETAL MUSCLE CONTRACTION BY CALCIUM
TWO ELEMENTARY MODELS FOR THE REGULATION OF SKELETAL MUSCLE CONTRACTION BY CALCIUM TERRELL L. HILL Laboratory ofmolecular Biology, National Institute ofarthritis, Diabetes, and Digestive and Kidney Diseases,
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature09450 Supplementary Table 1 Summary of kinetic parameters. Kinetic parameters were V = V / 1 K / ATP and obtained using the relationships max ( + m [ ]) V d s /( 1/ k [ ATP] + 1 k ) =,
More informationSINGLE-MOLECULE PHYSIOLOGY
SINGLE-MOLECULE PHYSIOLOGY Kazuhiko Kinosita, Jr. Center for Integrative Bioscience, Okazaki National Research Institutes Higashiyama 5-1, Myodaiji, Okazaki 444-8585, Japan Single-Molecule Physiology under
More informationikt kt x l ktk xl w1(r) could originate as a configurational entropy term, rather than as potential
PHASE TRANSITION IN A ONE-DIMENSIONAL SYSTEM, 11* BY TERRELL L. HILLt AND GEORGE M. WHITE DEPARTMENT OF CHEMISTRY, UNIVERSITY OF OREGON, EUGENE Communicated May 22, 1967 In the previous paper1 (Part I),
More informationStatistical mechanics of biological processes
Statistical mechanics of biological processes 1 Modeling biological processes Describing biological processes requires models. If reaction occurs on timescales much faster than that of connected processes
More informationIn biomolecular systems, free energy frequently needs to be
Kinetic equilibrium of forces and molecular events in muscle contraction Erwin W. Becker* Institut für Mikrostrukturtechnik, Forschungszentrum, and Universität Karlsruhe, 76021 Karlsruhe, P.O. Box 3640,
More informationInteractions and Dynamics within the Troponin Complex
Interactions and Dynamics within the Troponin Complex Tharin Blumenschein Steve Matthews Lab - Imperial College London (formerly Brian Sykes Lab, Canada) Striated muscle Thin filament proteins - regulation
More informationSarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle
Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle Bertrand C. W. Tanner 1, Thomas L. Daniel 2, Michael Regnier 1* 1 Department of Bioengineering, University of Washington, Seattle,
More informationSECOND PUBLIC EXAMINATION. Honour School of Physics Part C: 4 Year Course. Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS
2757 SECOND PUBLIC EXAMINATION Honour School of Physics Part C: 4 Year Course Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS TRINITY TERM 2013 Monday, 17 June, 2.30 pm 5.45 pm 15
More informationBinding Theory Equations for Affinity and Kinetics Analysis
Technology Note #101 Binding Theory Equations for Affinity and Kinetics Analysis This technology note summarizes important equations underlying the theory of binding of solute analytes to surface-tethered
More informationChapter 16. Cellular Movement: Motility and Contractility. Lectures by Kathleen Fitzpatrick Simon Fraser University Pearson Education, Inc.
Chapter 16 Cellular Movement: Motility and Contractility Lectures by Kathleen Fitzpatrick Simon Fraser University Two eukaryotic motility systems 1. Interactions between motor proteins and microtubules
More informationSupplementary Materials for
advances.sciencemag.org/cgi/content/full/1/9/e1500511/dc1 Supplementary Materials for Contractility parameters of human -cardiac myosin with the hypertrophic cardiomyopathy mutation R403Q show loss of
More informationBIOMECHANICS 3 Origins and consequences of forces in biological systems
BIOMECHANICS 3 Origins and consequences of forces in biological systems MOLECULAR MECHANISMS OF BIOLOGICAL MOVEMENT AT THE LEVELOF ORGANISMS MOLECULAR BASIS OF MUSCLE CONTRACTION DR. BEÁTA BUGYI - BIOPHYSICS
More informationTHALLIUM AND CESIUM IN MUSCLE CELLS COMPETE FOR THE ADSORPTION SITES NORMALLY OCCUPlED BY K+
THALLIUM AND CESIUM IN MUSCLE CELLS COMPETE FOR THE ADSORPTION SITES NORMALLY OCCUPlED BY K+ GILBERT N. LING Department of Molecular Biology. Pennsylvania Hospital. Philadelphia, Pennsylvania 19107 Reprit~red
More informationPhysical Models of Allostery: Allosteric Regulation in Capsid Assembly
Physical Models of Allostery: Allosteric Regulation in Capsid Assembly QCB Journal Club Prof. Sima Setayeshgar JB Holmes Nov. 2, 2017 Mechanisms of Allosteric Regulation From R.A. Laskowski, FEBS Letters,
More informationBiochemistry 3100 Sample Problems Binding proteins, Kinetics & Catalysis
(1) Draw an approximate denaturation curve for a typical blood protein (eg myoglobin) as a function of ph. (2) Myoglobin is a simple, single subunit binding protein that has an oxygen storage function
More informationChapter 10: Hemoglobin
Chapter 10: Hemoglobin Voet & Voet: Pages 320-353 Slide 1 Hemoglobin Function Larger aerobic (oxygen utilizing) organism require an O 2 transport system to deliver sufficient O 2 to tissues Dissolved O
More informationUse of Stable Analogs of Myosin ATPase Intermediates for Kinetic Studies of the Weak Binding of Myosin Heads to F-Actin
Biochemistry (Moscow), Vol. 64, No. 8, 1999, pp. 875-882. Translated from Biokhimiya, Vol. 64, No. 8, 1999, pp. 1043-1051. Original Russian Text Copyright 1999 by Rostkova, Moiseeva, Teplova, Nikolaeva,
More informationMuscle tissue. Types. Functions. Cardiac, Smooth, and Skeletal
Types Cardiac, Smooth, and Skeletal Functions movements posture and body position Support soft tissues Guard openings body temperature nutrient reserves Muscle tissue Special Characteristics of Muscle
More informationSUPPLEMENTARY INFORMATION
Figure S1. Secondary structure of CAP (in the camp 2 -bound state) 10. α-helices are shown as cylinders and β- strands as arrows. Labeling of secondary structure is indicated. CDB, DBD and the hinge are
More informationDecomposing Complex Cooperative Ligand Binding into Simple Components: Connections between Microscopic and Macroscopic models.
Decomposing Complex Cooperative Ligand Binding into Simple Components: Connections between Microscopic and Macroscopic models. Alexey Onufriev 1 and G. Matthias Ullmann, 1 Department of Computer Science,
More informationOur patient for the day...
Muscles Ch.12 Our patient for the day... Name: Eddy Age: Newborn Whole-body muscle contractions No relaxation Severe difficulty breathing due to inadequate relaxation of breathing muscles Diagnosed with
More informationSECOND PUBLIC EXAMINATION. Honour School of Physics Part C: 4 Year Course. Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS
2757 SECOND PUBLIC EXAMINATION Honour School of Physics Part C: 4 Year Course Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS TRINITY TERM 2011 Monday, 27 June, 9.30 am 12.30 pm Answer
More informationAnatoly B. Kolomeisky. Department of Chemistry CAN WE UNDERSTAND THE COMPLEX DYNAMICS OF MOTOR PROTEINS USING SIMPLE STOCHASTIC MODELS?
Anatoly B. Kolomeisky Department of Chemistry CAN WE UNDERSTAND THE COMPLEX DYNAMICS OF MOTOR PROTEINS USING SIMPLE STOCHASTIC MODELS? Motor Proteins Enzymes that convert the chemical energy into mechanical
More informationPHYSIOLOGY CHAPTER 9 MUSCLE TISSUE Fall 2016
PHYSIOLOGY CHAPTER 9 MUSCLE TISSUE Fall 2016 2 Chapter 9 Muscles and Muscle Tissue Overview of Muscle Tissue types of muscle: are all prefixes for muscle Contractility all muscles cells can Smooth & skeletal
More informationThermal Denaturation and Aggregation of Myosin Subfragment 1 Isoforms with Different Essential Light Chains
Int. J. Mol. Sci. 21, 11, 4194-4226; doi:1.339/ijms11114194 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-67 www.mdpi.com/journal/ijms Article Thermal Denaturation and Aggregation of
More informationFree Energy. because H is negative doesn't mean that G will be negative and just because S is positive doesn't mean that G will be negative.
Biochemistry 462a Bioenergetics Reading - Lehninger Principles, Chapter 14, pp. 485-512 Practice problems - Chapter 14: 2-8, 10, 12, 13; Physical Chemistry extra problems, free energy problems Free Energy
More informationPhysics of Cellular materials: Filaments
Physics of Cellular materials: Filaments Tom Chou Dept. of Biomathematics, UCLA, Los Angeles, CA 995-766 (Dated: December 6, ) The basic filamentary structures in a cell are reviewed. Their basic structures
More information2: CHEMICAL COMPOSITION OF THE BODY
1 2: CHEMICAL COMPOSITION OF THE BODY Although most students of human physiology have had at least some chemistry, this chapter serves very well as a review and as a glossary of chemical terms. In particular,
More informationDescription: Supplementary Figures, Supplementary Methods, and Supplementary References
File Name: Supplementary Information Description: Supplementary Figures, Supplementary Methods, and Supplementary References File Name: Supplementary Movie 1 Description: Footage of time trace of seeds
More informationNucleosome Switching
Nucleosome Switching David J. Schwab, Robijn F. Bruinsma, Joseph Rudnick Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA, 90024 & Jonathan Widom Department of
More informationSupramolecular Chemistry of Nanomaterials
Supramolecular Chemistry of Nanomaterials Joachim Steinke Ramon Vilar Lecture 6 Towards the Development of Molecular Machines Department of Chemistry Imperial College of Science, Technology and Medicine
More informationChromatography Outline
Chem 2001 Summer 2004 Outline What is? The Chromatogram Optimization of Column Performance Why Do Bands Spread? Gas High-Performance Liquid Ion-Exchange 2 What is? In chromatography, separation is achieved
More informationSwelling and Collapse of Single Polymer Molecules and Gels.
Swelling and Collapse of Single Polymer Molecules and Gels. Coil-Globule Transition in Single Polymer Molecules. the coil-globule transition If polymer chains are not ideal, interactions of non-neighboring
More informationSlow symmetric exchange
Slow symmetric exchange ϕ A k k B t A B There are three things you should notice compared with the Figure on the previous slide: 1) The lines are broader, 2) the intensities are reduced and 3) the peaks
More informationA simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations
A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations Michal Vieth Department of Chemistry, The Scripps Research Institute, 10666 N. Torrey Pines Road,
More informationBRIEF COMMUNICATION BLOCKING OF INWARD RECTIFICATION. A MODEL FOR THE EFFECTS OF POTENTIAL AND EXTERNAL K+ CONCENTRATION ON THE Cs+
BRIEF COMMUNICATION A MODEL FOR THE EFFECTS OF POTENTIAL AND EXTERNAL K+ CONCENTRATION ON THE Cs+ BLOCKING OF INWARD RECTIFICATION S. CIANI, S. KRASNE, AND S. HAGIWARA, Department ofphysiology, Ahmanson
More informationSupplementary Information. Overlap between folding and functional energy landscapes for. adenylate kinase conformational change
Supplementary Information Overlap between folding and functional energy landscapes for adenylate kinase conformational change by Ulrika Olsson & Magnus Wolf-Watz Contents: 1. Supplementary Note 2. Supplementary
More informationBioelectricity Prof. Mainak Das Department of Biological Sciences, and Bioengineering Indian Institute of Technology, Kanpur.
Bioelectricity Prof. Mainak Das Department of Biological Sciences, and Bioengineering Indian Institute of Technology, Kanpur Lecture 17 Welcome back to the bioelectricity lecture, series. So, in the last
More informationExchange of Counterions in DNA Condensation. Abstract
Exchange of Counterions in DNA Condensation Yoshihiro Murayama and Masaki Sano Department of Physics, University of Tokyo, Tokyo 113-0033, Japan Abstract We measured the fluorescence intensity of DNA-bound
More informationThe molecular basis of cardiac mechanics: Regulation of motor unit recruitment.
1of 4 The molecular basis of cardiac mechanics: Regulation of motor unit recruitment. C. Levy, A. Landesberg Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
More informationIntroduction to Metabolism (Or Energy Management) Chapter 8
Introduction to Metabolism (Or Energy Management) Chapter 8 Metabolism of the chemical reactions in the organism Building up molecules Breaking down molecules Managing energy and materials Route to end-product
More informationChapter 6- An Introduction to Metabolism*
Chapter 6- An Introduction to Metabolism* *Lecture notes are to be used as a study guide only and do not represent the comprehensive information you will need to know for the exams. The Energy of Life
More informationPauli Deformation APPENDIX Y
APPENDIX Y Two molecules, when isolated say at infinite distance, are independent and the wave function of the total system might be taken as a product of the wave functions for the individual molecules.
More informationOperation modes of the molecular motor kinesin
PHYSICAL REVIEW E 79, 011917 2009 Operation modes of the molecular motor kinesin S. Liepelt and R. Lipowsky Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany *
More informationAffinity labels for studying enzyme active sites. Irreversible Enzyme Inhibition. Inhibition of serine protease with DFP
Irreversible Enzyme Inhibition Irreversible inhibitors form stable covalent bonds with the enzyme (e.g. alkylation or acylation of an active site side chain) There are many naturally-occurring and synthetic
More informationLigand Binding A. Binding to a Single Site:
A. Binding to a Single Site: The uilibrium constant (also known as association constant or affinity constant) for the binding of a ligand to a protein is described by the following uation (note: A ): [
More informationModeling. EC-Coupling and Contraction
Bioeng 6460 Electrophysiology and Bioelectricity Modeling of EC-Coupling and Contraction Frank B. Sachse fs@cvrti.utah.edu Overview Quiz Excitation-Contraction Coupling Anatomy Cross Bridge Binding Coupling
More informationPart II => PROTEINS and ENZYMES. 2.7 Enzyme Kinetics 2.7a Chemical Kinetics 2.7b Enzyme Inhibition
Part II => PROTEINS and ENZYMES 2.7 Enzyme Kinetics 2.7a Chemical Kinetics 2.7b Enzyme Inhibition Section 2.7a: Chemical Kinetics Synopsis 2.7a - Chemical kinetics (or reaction kinetics) is the study of
More informationName: Date: Period: Biology Notes: Biochemistry Directions: Fill this out as we cover the following topics in class
Name: Date: Period: Biology Notes: Biochemistry Directions: Fill this out as we cover the following topics in class Part I. Water Water Basics Polar: part of a molecule is slightly, while another part
More informationActo-myosin: from muscles to single molecules. Justin Molloy MRC National Institute for Medical Research LONDON
Acto-myosin: from muscles to single molecules. Justin Molloy MRC National Institute for Medical Research LONDON Energy in Biological systems: 1 Photon = 400 pn.nm 1 ATP = 100 pn.nm 1 Ion moving across
More informationMolecular Driving Forces
Molecular Driving Forces Statistical Thermodynamics in Chemistry and Biology SUBGfittingen 7 At 216 513 073 / / Ken A. Dill Sarina Bromberg With the assistance of Dirk Stigter on the Electrostatics chapters
More informationInteraction of Lys-61 Labeled Actin with Myosin Subfragment-1 and the Regulatory Proteins1
J. Biochem. 106, 651-655 (1989) Interaction of Lys-61 Labeled Actin with Myosin Subfragment-1 and the Regulatory Proteins1 Masao Miki Muscle Research Unit, Department of Anatomy, University of Sydney,
More informationTHE EFFECT OF TEMPERATURE ON THE TITRATION CURVE OF CASEIN
THE EFFECT OF TEMPERATURE ON THE TITRATION CURVE OF CASEIN BY V. A. PERTZOFF Az o S. C. CARPENTER (From the Chemical Laboratories, Harvard University, Cambridge) (Accepted for publication, July 11, 1932)
More informationLecture 2: Receptor-ligand binding and cooperativity
Lecture 2: Receptor-ligand binding and cooperativity Paul C Bressloff (Spring 209) A biochemical receptor is a protein molecule that receives a chemical signal in the form of ligand molecules. The ligands
More informationEFFECT OF Ca ION CONCENTRATION ON CROSS- BRIDGE KINETICS IN RABBIT PSOAS FIBERS
EFFECT OF Ca ION CONCENTRATION ON CROSS- BRIDGE KINETICS IN RABBIT PSOAS FIBERS EVIDENCE FOR THE PRESENCE OF Two Ca-ACTIVATED STATES OF THIN FILAMENT MASATAKA KAWAI, ROBERT N. COX, AND PHILIP W. BRANDT,
More informationMichaelis Menten Kinetics- Identical Independent Binding Sites
Michaelis Menten Kinetics- Identical Independent Binding Sites Dr. M. Vijayalakshmi School of Chemical and Biotechnology SASTRA University Joint Initiative of IITs and IISc Funded by MHRD Page 1 of 8 Table
More informationComputational Stiffness Method
Computational Stiffness Method Hand calculations are central in the classical stiffness method. In that approach, the stiffness matrix is established column-by-column by setting the degrees of freedom
More informationModelling Muscle Contraction a multiscale approach
Porto Ercole, M&MKT 2016 Multiscale Systems from Particles to Continuum: Modelling and Computation Modelling Muscle Contraction a multiscale approach Giovanni Naldi Dipartimento di Matematica ``F. Enriques
More informationChapter 8: An Introduction to Metabolism. 1. Energy & Chemical Reactions 2. ATP 3. Enzymes & Metabolic Pathways
Chapter 8: An Introduction to Metabolism 1. Energy & Chemical Reactions 2. ATP 3. Enzymes & Metabolic Pathways 1. Energy & Chemical Reactions 2 Basic Forms of Energy Kinetic Energy (KE) energy in motion
More informationChapter 8: An Introduction to Metabolism
Chapter 8: An Introduction to Metabolism Key Concepts 8.1 An organism s metabolism transforms matter and energy, subject to the laws of thermodynamics 8.2 The free-energy change of a reaction tells us
More informationChemistry 5.07SC Biological Chemistry I Fall Semester, 2013
Chemistry 5.07SC Biological Chemistry I Fall Semester, 2013 Lecture 10. Biochemical Transformations II. Phosphoryl transfer and the kinetics and thermodynamics of energy currency in the cell: ATP and GTP.
More informationOn the Use of the Hill Functions in Mathematical Models of Gene Regulatory Networks
Math. Model. Nat. Phenom. Vol. 3, No. 2, 2008, pp. 85-97 On the Use of the Hill Functions in Mathematical Models of Gene Regulatory Networks M. Santillán 1 Centro de Investigación y de Estudios Avanzados
More informationSubstrate-dependent switching of the allosteric binding mechanism of a dimeric enzyme
Supplementary Information: Substrate-dependent switching of the allosteric binding mechanism of a dimeric enzyme Lee Freiburger, 1 Teresa Miletti, 1 Siqi Zhu, 1 Oliver Baettig, Albert Berghuis, Karine
More informationChemical Exchange and Ligand Binding
Chemical Exchange and Ligand Binding NMR time scale Fast exchange for binding constants Slow exchange for tight binding Single vs. multiple binding mode Calcium binding process of calcium binding proteins
More informationTHE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION
THE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION AND CALIBRATION Calculation of turn and beta intrinsic propensities. A statistical analysis of a protein structure
More informationStretching lattice models of protein folding
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 2031 2035, March 1999 Biophysics Stretching lattice models of protein folding NICHOLAS D. SOCCI,JOSÉ NELSON ONUCHIC**, AND PETER G. WOLYNES Bell Laboratories, Lucent
More informationLEARNING OBJECTIVES SEPARATION SCIENCE CHEMICAL EQUILIBRIUM UNIT
LEARNING OBJECTIVES SEPARATION SCIENCE CHEMICAL EQUILIBRIUM UNIT Thomas Wenzel, Bates College Introductory Material After the introductory material covered in the text and lecture form, the student will
More informationThe Riboswitch is functionally separated into the ligand binding APTAMER and the decision-making EXPRESSION PLATFORM
The Riboswitch is functionally separated into the ligand binding APTAMER and the decision-making EXPRESSION PLATFORM Purine riboswitch TPP riboswitch SAM riboswitch glms ribozyme In-line probing is used
More informationFig. 1. Stereo images showing (A) the best fit of the atomic model for F actin and the F actin map obtained by cryo-em and image analysis, and (B) goo
Fig. 1. Stereo images showing (A) the best fit of the atomic model for F actin and the F actin map obtained by cryo-em and image analysis, and (B) good correspondence between the location of Cys374 and
More informationChapter 5. Energy Flow in the Life of a Cell
Chapter 5 Energy Flow in the Life of a Cell Including some materials from lectures by Gregory Ahearn University of North Florida Ammended by John Crocker Copyright 2009 Pearson Education, Inc.. Review
More informationModeling the energy transfer pathways. Creatine kinase activities and heterogeneous distribution of ADP in the perfused heart.
Modeling the energy transfer pathways. Creatine kinase activities and heterogeneous distribution of ADP in the perfused heart. Joubert, F., Hoerter, J.A. and M azet, J.-L. U446 INSERM, Université Paris-Sud,
More informationGround Rules of Metabolism CHAPTER 6
Ground Rules of Metabolism CHAPTER 6 Antioxidants You ve heard the term. What s the big deal? Found naturally in many fruits and vegetables Added to many products What do they actually do? Antioxidants
More informationChapter 5. Directions and Rates of Biochemical Processes
Chapter 5 Directions and Rates of Biochemical Processes Key Questions What factors determine which way a reaction will go? What factors determine the rate of a chemical reaction? How do enzymes work? How
More informationBSc and MSc Degree Examinations
Examination Candidate Number: Desk Number: BSc and MSc Degree Examinations 2018-9 Department : BIOLOGY Title of Exam: Molecular Biology and Biochemistry Part I Time Allowed: 1 hour and 30 minutes Marking
More information1 Adsorption of NO 2 on Pd(100) Juan M. Lorenzi, Sebastian Matera, and Karsten Reuter,
Supporting information: Synergistic inhibition of oxide formation in oxidation catalysis: A first-principles kinetic Monte Carlo study of NO+CO oxidation at Pd(100) Juan M. Lorenzi, Sebastian Matera, and
More informationSupporting Information Converter domain mutations in myosin alter structural kinetics and motor function. Hershey, PA, MN 55455, USA
Supporting Information Converter domain mutations in myosin alter structural kinetics and motor function Laura K. Gunther 1, John A. Rohde 2, Wanjian Tang 1, Shane D. Walton 1, William C. Unrath 1, Darshan
More informationCHAPTER 8. An Introduction to Metabolism
CHAPTER 8 An Introduction to Metabolism WHAT YOU NEED TO KNOW: Examples of endergonic and exergonic reactions. The key role of ATP in energy coupling. That enzymes work by lowering the energy of activation.
More informationLecture 19 (10/30/17) Enzyme Regulation
Reading: Ch5; 164, 166-169 Problems: none Remember Today at 6:30 in PHO-206 is the first MB lecture & quiz NEXT Reading: Ch5; 158-169, 162-166, 169-174 Lecture 19 (10/30/17) Problems: Ch5 (text); 3,7,8,10
More informationAdsorption Equilibria. Ali Ahmadpour Chemical Eng. Dept. Ferdowsi University of Mashhad
Adsorption Equilibria Ali Ahmadpour Chemical Eng. Dept. Ferdowsi University of Mashhad Contents Introduction Adsorption isotherm models Langmuir isotherm Volmer isotherm Fowler-Guggenheim isotherm Hill-deBoer
More informationSupporting Text - Jégou et al.
Supporting Text - Jégou et al. I. PAUSES DURING DEPOLYMERIZATION Pauses were observed during the ymerization of individual filaments grown from ADP-, CrATP- or MgATPactin, in the presence or in the absence
More information