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* State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130021, People's Republic of China; and
Department of Chemistry and Physics, State University of New York, Stony Brook, New York 11794
Correspondence: Address reprint requests to Jin Wang, E-mail: jin.wang.1{at}stonybrook.edu.
| ABSTRACT |
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| INTRODUCTION |
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According to the energy landscape theory, in general at the initial stage of folding, there are multiple paths toward native state. The discrete paths emerge only when the landscape becomes rough and local traps are important at late stage of folding. Searching for kinetic paths has been a central issue for the folding experimental community for many years (6
18
). Unfortunately, most of the current kinetic folding studies are formulated in terms of the rate dynamics giving only the end results, rather than the paths that represent the full intermediate histories connecting the initial and final ends. It is, therefore, important and natural to formulate the theory in terms of path language. Such a formulation would help to resolve the challenging kinetic path issue of the folding problem and provide a direct tool and language for the theoretical and experimental community to understand each other better. Another advantage of using paths is that the direct integration over paths is normally easier computationally than solving differential equations locally in microscopic details.
Path integral methods since first appearing (19
,20
) have been successfully applied to many areas in physics (20
22
) and chemistry (23
25
). There are so far very limited studies on folding paths. Wang et al. (4
) have studied a downhill folding process (very steep funnel) without activation barrier. It is shown that there exists a multiple path to discrete path transition at a temperature higher than the thermodynamic glassy trapping temperature. The relevance to single molecule dynamics is studied (26
,27
). Olender and Elber and Elber et al. (28
,29
) studied peptide folding with atomic level simulations and identify some key paths. The purpose of this study is to formulate a diffusive path integral framework for the general case where there exists activation free-energy barriers on the folding landscape, and to identify and quantify the dominant path contributions to the kinetics.
| METHOD AND MATHEMATICAL DETAILS |
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Let us turn to a model Hamiltonian that describes protein folding. To first order approximation, we assume that the energetics that favors bringing two or multiple residues close together from the protein is due mainly to the short-range (in space) hydrophobic driving force. The form of the interactions is
ijk...p(
i,
j,
k, ...
p, ri, rj, rk, ..., rp), where
ijk...p is the multibody coupling strength, ri is the position of the ith residue, and
i represents the physical properties of the residue i, for example, hydrophobic charges, etc. Here, we also assume that the environmental solvent effects are already averaged out, resulting in the multibody cooperative hydrophobic interactions among residues upon folding.
We may write down the Hamiltonian energy function of a polypeptide sequence as:
![]() | (1) |
ijk...p = 1 when there is a multibody contact adjacent in space made among monomers ijk...p and
ijk...p = 0 otherwise.
is up to N, N is the length of the polypeptide sequence, and Eijk...p is quite random due to the sequence and interaction heterogeneity. Notice that this is mathematically closely related to the random energy model (30
Suppose there exists a native configurational state n of energy En. We can find the probability that configuration a has energy Ea, given that a has an overlap Q with n, where Q is the fraction of native contacts of state a:
and N is the total number of native contacts. Q can be used as an order parameter or a reaction coordinate for the physical folding process that measures how close the states are toward native state. Note that for Q = 1, the state is in the native folded state and for Q = 0, the configurations are in totally nonnative unfolded states.
The conditional probability is obtained directly by averaging over the Gaussian distribution of contact energy
ijk...p (
). By approximating the cooperative multibody interactions
ijk...p in the Hamiltonian into the factorization of pair interaction terms
ij
jk... through a suitable decomposition law such as in the superposition approximation in the theory of fluid, the expression can be simplified as:
where m is the order of the interactions (m = 2 for two-body interactions, m = 3 for three-body interactions, and m = p for p-body interactions),
is the average mean energy, and 
is the effective width of the energy distribution per contact.
The configurational entropy Stot as a function of similarity Q with a given state is treated in details by the previous studies (32
,33
).
Given the Stot(Q) and conditional probability distribution obtained earlier, the average numbers of states of energy E and overlap Q with native state n is:
This is effectively the microcanonical ensemble description of the thermodynamics. At each stratum of the order parameter or reaction coordinate Q, the set of states is modeled by a random energy model. By the thermodynamic relation of
we can obtain the energy and entropy of the biomolecular folding as:
and
where stot(Q) = Stot(Q)/N. The entropy vanishes at a characteristic temperature:
which signals the trapping of the polypeptide chain into a low-energy conformational state within the stratum characterized by Q. Notice that when Q = 0 (nonnative unfolded states),
From the thermodynamic expression of the energy and the entropy given above, we can easily obtain the expression for the free energy per contact as (33
):
where
The free energy is composed of three terms, the entropy, the native driving force, and roughness contribution of the energy landscape. In the parameter space in (
n, 
, T), the expression above can have a double minimum structure in the reaction coordinate Q with one minimum at low Q corresponding to the nonnative states separated by a barrier from another minimum at high Q corresponding to the native folded state. As the cooperativity measured by multibody interaction order m increases, the free-energy minimum of nonnative states and native folded state shift toward Q
0 and Q
1, respectively. To the extent that this approximation is good (m 
), we can equate the free energies of the nonnative states and native folding state to obtain the folding transition temperature (F(Q = 0) = F(Q = 1)):
![]() |
Take the ratio of folding temperature and trapping temperature, we obtain:
![]() | (2) |
is the ratio of the energy gap between native state and the average of the energy landscape spectrum to the ruggedness or the width (spread) of the distribution of the energy landscape spectrum weighted by entropy per contact
which is on the order of 1 (34
should be maximized; this, in turn, leads to the maximization of
. Therefore, maximizing the ratio of the energy gap (or the slope) versus the roughness of the underlined energy landscape becomes the criterion for the thermodynamic stability of folding, implying a funneled energy landscape.
Under the free-energy profiles, the equation of motion for native contact Q formation can be formulated as:
![]() | (3) |
is the friction coefficient;
F(Q)/
Q is the gradient force the motion of Q would follow. Due to the long timescale of folding compared with the short timescale fluctuations, the folding can be seen as overdamped. Therefore, the second derivatives of Q with respect to time t is ignored;
is assumed to be a Gaussian noise force term where its correlation becomes 
(Q, t)
(Q, 0)
= 2D(Q)
(t). D(Q) is the Q-dependent diffusion coefficient. The noise term is related to the environmental fluctuations (temperature) through the Einstein relationship (fluctuation dissipation theorem) D(Q)
= kBT. The protein folding has many degrees of freedom, therefore, when looking at the motion along the reduced one-dimensional order parameter or reaction coordinate Q, the noise is effectively from the rest of the other multidimensions of folding and the environments surrounding it.
When taking into account the combination of multibody interactions (up to the six-body interactions because the order of the hydrophobic multibody interactions beyond two-body interactions is typically ranging from three or four up to six), the free energy becomes:
![]() | (4) |
, c1, c2, c3, 1
c1 c2 c3 are the coefficient mimicking the relative importance of the order of multibody (2
S0(1 Q) QLog(Q) (1 Q)Log(1 Q), where S0
ln(10/2.718); 10 in the ln is the degrees of freedom per residue whereas factor 2.718 in the ln takes into account the constraints of the phase space upon collapse. The first term of the entropy is the entropy loss forming a contact whereas the rest of the two terms is responsible for the entropy associated with the possible ways of forming a contact.
We can now formulate the dynamics with the Onsager-Machlup (21
) functional path integral as:
![]() | (5) |
The DQ is summing over all possible paths connecting Qi at time t = 0 to Qf at time t. The exponential factor gives the weight of each path, so the probability of folding dynamics from nonnative configuration Qi to native configuration Qf is equal to the sum of the weights from the contributions of all the possible paths. L(Q(t)) is the Lagrangian of the system.
Each path in the path integral contributes a weight, but not every path gives the same contribution. In fact, the contribution from the paths to the weight is on the exponential, so the dominant paths with the largest weight contribute significantly larger than the ones with the subdominant or even smaller weights. We can then approximate the path integrals with a set of dominant paths and ignore the subleading terms. One can easily see to find the paths with the optimal weights, the dominant paths should satisfy the Euler-Lagrangian equation (see Fig. 1):
![]() | (6) |
![]() | (7) |
![]() | (8) |
|
![]() | (9) |
as kinetic energy term with position Q dependent mass and U = V as the effective potential, and E as the total energy. The problem becomes a one-dimensional particle moving in a potential well U. The free energy as a function of Q at various temperatures T is plotted in Fig. 2, AC, (for mixed but mainly four-body, five-body, and six-body interactions). The potential V as a function of Q is plotted in Fig. 3, AC (for mixed but mainly four-body, mixed but mainly five-body, and mixed but mainly six-body interactions) as a function of Q at folding temperature Tf.
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![]() | (10) |
at t = 0) and the integral is from the beginning of one instanton at t = 0 and at Qmin to the end of one instanton at the bounce-back point Qmax and at tmax. Qmin and Qmax correspond to approximately the minimum of V near the nonnative state and the bounce-back point of V near the native folded state, where the value of V at the bounce-back point is equal to that of the minimum of V.
|
![]() | (11) |
The above expression can be easily evaluated in the Laplace representation s:
![]() | (12) |
By inverting the Laplace transform, we obtain:
![]() | (13) |
+ and
are given by:
![]() | (14) |
When V(Qmin) = V(Qmax) as is the case in instantons, the expression is simplified as:
![]() | (15) |
| DISCUSSIONS AND CONCLUSIONS |
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= 1, the bias or slope of the landscape toward folded state 
= 3 and
= 0.05, c1 = 0.05, c2 = 0, c3 = 0, and 1
c1 = 0.90 (for mixed two-, three-, and four-body interactions, but dominant four-body interactions);
= 0.05, c1 = 0.05, c2 = 0.05, c3 = 0, and 1
c1 c2 = 0.85 (for mixed two-, three-, four-, and five-body interactions, but dominant five-body interactions);
= 0.05, c1 = 0.05, c2 = 0.05, c3 = 0.05, and 1
c1 c2 c3 = 0.80 (for mixed two-, three-, four-, five-, and six-body interactions, but dominant six-body interactions). The diffusion coefficients are given as (40
E(Q)2] for 2Tg < T; and D(Q) = D0exp[S0(Q) + (ßg(Q) ß)2]
E(Q)2] for Tg < T < 2Tg. Here,
Fig. 4, AC, shows the multiinstanton solutions at T = Tf for dominant four-, five-, and six-body interactions, respectively. Fig. 5, A and B, show the temperature dependence of the logarithm (ln) of the folding rate (K) lnK for dominant four-, five-, and six-body interactions when diffusion coefficient is constant with D = D(Q = 0) and when diffusion coefficient is reaction coordinate dependent with D = D(Q).
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This indicates that the kinetics is not only controlled by the inherent thermodynamic free energy but also by the diffusion. This is particularly important because the fast folding experiments are now approaching the speed limit where the kinetics of pure diffusion can be measured (47
,15
,48
).
We can simplify the expression of the kinetic rate by assuming that diffusion coefficient is relatively small. In this case, we can substitute the instanton solution to the action of the probability expression of the path integral (49
) and obtain analytic form of equilibrium probability as:
![]() | (16) |
![]() | (17) |
The effective activation energy for transitions from nonnative unfolded state at Q = Qmin to the transition state Q# is given by:
![]() | (18) |
It is very important to realize that the current formalism implies both the diffusion and thermodynamic free-energy barrier control the kinetics of protein folding as mentioned above. When the underlying process is barrier limited, both the thermodynamic barrier and diffusion contribute to the kinetics although free energy contribution might be larger. The role of diffusion is to modify the effective free-energy profile and the corresponding barrier. In the case where there is no inherent free energy barrier, the kinetics is controlled by diffusion. Thus, the formalism in this article provides a route to look for the switching roles from thermodynamic-barrier-driven kinetics to downhill diffusion-driven kinetics, which is quite relevant for the experimental study of fast folding proteins where the speed of folding is determined from the thermodynamic-driven to the essentially diffusion-controlled process (47
,15
,48
).
The current formalism can also be used to discuss the transition state property of protein folding. In the case of constant diffusion, the current formalism reduces to the normal transition state theory and kinetics is controlled by the free energy barrier. As mentioned above, when the diffusion coefficient is not a constant, the kinetics is controlled by both the free energy barrier and diffusion. In the case when the thermodynamic barrier is large, the kinetics is dominated by the free energy profile. On the other hand, when the thermodynamic barrier is moderate, the effect of diffusion will come into play by modifying the original free energy profile. Both the position and value of the resulting effective transition state free energy will be shifted. So the kinetics will be modified by this shift of the original transition state. Details of the study will be given in a future publication.
Let us discuss the possible connections of our approach with another set of experimental observations (50
). When the diffusion coefficient is a constant, the kinetics is controlled by the free energy profile as we have derived above. In the barrier limited case, if the barrier is caused mainly by topology instead of heterogeneity of the interactions, then the free energy barrier is mainly from entropy contribution of loop contacts (32
,33
,51
). Thus, the free energy change with respect to the mean sequence length of making contacts
can be shown as:
![]() | (19) |
Thus, the free energy barrier is linked to the average sequence length of making the contacts
The effect of increasing the mean loop length is to increase the barrier height. So the kinetics is faster (slower) when the mean contact distance is small (large). When the diffusion coefficient is not constant and interaction heterogeneity are taken into account, the free energy dependence on the mean contact distance might not be as strong. Further detailed investigations on this are needed and will be carried out in a future publication.
We discussed in this article the long-time dynamics of folding. In principle, the short-time dynamics can be revealed by solving the Euler-Lagrangian equation for the optimal paths. Because the time is short, the solutions typically don't have enough time forming multiple instantons. Finding dominant paths becomes solving ordinary differential equation for fixing two end points. One can expand around the dominant solution up to quadratic order and obtain the contribution to the probability of folding. In general the results are good for short times and the kinetics is usually nonexponential. This is in contrast with the long-time case where the dynamics is usually controlled by the longest timescale as we discussed here.
We obtain in this study the optimal instanton paths that determines the folding rate dynamics in the long time limit. We should mention that the optimal paths are actually a set of paths in the multidimensional configurational space. They represent the dominant flow of paths directed toward the native state. At low temperatures, the folding might be trapped into the local valleys, while the current continuous path approach can give some qualitative features as to approximately when the continuous flow of paths might break down; instead, the more appropriate approach seems to be the discrete version of the path integral we presented here. The formulation is currently under development. With this formulation, one can study and understand the transition from the multiple paths to the discrete path transition in the case of activated folding transition.
The kinetic rate dynamics is often studied by the Fokker-Planck type rate equations (or Brownian dynamics). This approach to the kinetics is mathematical, related to the path integral formulations presented here but emphasizing different aspects. Although the path method concentrates on intermediate processes and the corresponding contributions to the final kinetics, the Fokker-Planck type rate equation approach concentrates more on the end results. Therefore, it is convenient and advantageous to address the kinetic path issues for protein folding in the path integral formulation.
It is worth mentioning that biomolecular recognition (binding) often involves large fluctuations and conformational changes (52
59
); sometimes local unfolding (60
,61
) for induced fit (62
) is necessary, so in general folding and binding are dynamically coupled. It is tempting to study the kinetics of the folding-binding process using the current developed path integral methodology (J. Wang, K. Zhang, H. Y. Lu, and E. K. Wang, unpublished data). The crucial question would be what are the dominant kinetic paths for the folding-binding process in nature.
| ACKNOWLEDGEMENTS |
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The work of J.W. is supported by National Science Foundation Career Award, Petroleum Research Fund, K. C. Wong Foundation Research Award, and Stony Brook Faculty Funding. The work of K.Z., H.L., and E.K.W. is supported by the Chinese National Science Foundation.
Submitted on October 28, 2004; accepted for publication June 17, 2005.
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