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Physics Department, National Taiwan Normal University, Taipei, Taiwan, Republic of China
Correspondence: Address reprint requests to Chi-Ming Chen, 88 Sec. 4 Ting-Chou Rd., Taipei, Taiwan, 11718. Tel.: 886-2-86638109; E-mail: cchen{at}phy.ntnu.edu.tw.
| ABSTRACT |
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helices for both random folding and assisted folding. The chain length dependence of the folding time of a hydrophobic segment to a helical state is studied for both free and anchored chains. An unusual length dependence in the folding time of anchored chains is observed. | INTRODUCTION |
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helices (Cantor and Schimmel, 1980
Membrane proteins (MPs) perform important and diverse functions in living cells, such as regulation, communication, and assisting the folding of other MPs (for a review, see White and Wimley, 1999
). They are partially buried in the nonpolar environment of a lipid bilayer, where the hydrophobic effect is absent. Because lipid tails are unable to form hydrogen bonds with proteins, the intrachain hydrogen bonding along the backbone of proteins in a membrane plays a significant role in forming their native structure. According to the structure of transmembrane segments, there are two known classes of MPs. The first class contains MPs whose transmembrane segments all form an
-helical structure with lengths (Nc) of 17 to 25 amino acids (aa). In the second class, on the other hand, those MPs usually have a ß-barrel structure. However, due to difficulties in crystallizing MPs, only a dozen or so MPs have known crystallographic structures so far. Among them, helix bundles are much more abundant than ß barrels.
A previous model using a full-backbone atom representation in a diamond lattice initiates an interesting study on the insertion of polypeptides into a membrane (Milik and Skolnick, 1992
). This model explicitly specifies that hydrogen bonds can form for only (i, i ± 4) pairs, where i labels amino acids in the chain. This can be considered as an extreme case in emphasizing the (i, i ± 4) hydrogen bonding state because there is no reason to forbid hydrogen bonding between (i, i ± n) residues for n > 4. Furthermore, this restriction also excludes the possibility to form ß strands. Our previous paper (Chen, 2001
) proposes a lattice model for the folding of transmembrane polypeptides, in which the backbone hydrogen bonding of polypeptides can occur between i and i ± n for n
4. Our model predicts two possible stable structures of transmembrane polypeptides, including helix and double helix structures, which have been observed for gramicidin dimers (Arumugam et al., 1996
). However, the folding time of a polypeptide chain in this simple model is unexpectedly long, which might result from its incapability to distinguish the differences among various hydrogen bonding states. In this paper, we propose a lattice model of MPs to study their native structures and cooperative folding. The main goal of our model is to predict the native structures of membrane proteins by their relevant physical interactions alone, and this model is then reliable for us to study the folding kinetics of a transmembrane peptide with minimal artifacts. Predicted structures of MPs from our model can be refined by all-atom models and will be useful in studying their biological functions by docking studies. This model has a composite energy function to describe interactions among amino acids, which uses realistic interactions when residues are in a membrane but statistical potentials when they are in water. We show that this model predicts a reasonably good native structure of sensory rhodopsin I (SRI), which is a phototaxis receptor in Halobacterium salinarum and consists of 239 amino acids. In addition, we study the cooperative effect on the folding time of MPs by introducing a cooperative factor to favor the (i, i ± 4) hydrogen bonding state. Our chain representation is based on the bond-fluctuation model (Carmesin and Kremer, 1988
; Chen and Fwu, 2001
; Chen, 2001
), which has advantages of giving reasonably good secondary structures and of simulating a more realistic diffusive kinetics than regular lattice models, while the computational cost is still quite limited compared to that of off-lattice models. We note that, although a helix bundle structure is studied in this paper, our model can also be used to predict ß-barrel structures because backbone hydrogen bonding is possible for amino acids far apart from each other in the sequence.
| MODEL |
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i,j
|(ni rij) (nj rij)|
r(i,j),4, where ni is the N
i (1 - cos
i), where e1 is the bending rigidity and
i is the angle between two consecutive bonds i and i + 1. The vdW interaction between amino acids is modeled by Evdw = e2 
i,j
{[1.78/r(i,j)]12 - [1.78/r(i,j)]6}, where e2 is its strength relative to hydrogen bonding. This vdW term has a minimum if two amino acids are next to each other in a cubic lattice model. For amino acids in water, their interactions are modeled by a residue-residue contact potential (Econtact) and the hydropathical interaction (Ehydropathy), i.e., Uwater = Econtact + Ehydropathy. The interactions between the exposed residues and the lipid bilayer are ignored. Here we use the Thomas-Dill contact potential with strength e3 to model the residue-residue interaction in water when residues are in contact (Thomas and Dill, 1996
i li2) in the membrane, where li is the projected length of the i-th transmembrane segment on the membrane surface (Chen, 2001| ALGORITHM OF SIMULATIONS |
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Each monomer in the model is a cube of length 1 (lattice spacing) on a cubic lattice as shown in Fig. 1. The set of allowed bond vectors is B = P(2,0,0)
P(2,1,0)
P(2,1,1)
P(2,2,1)
P(3,0,0)
P(3,1,0), where P(a,b,c) stands for the set of all permutations and sign combinations of ±a, ±b, ±c. The number of configurations per bond is z = 108. The length of one bond can take any one of the five values 2, 51/2, 61/2, 3, 101/2 (in units of lattice spacing). Chains satisfy the excluded volume constraint: no lattice site may be occupied by more than one monomer. The set B is chosen to satisfy the constraints of both excluded volume between monomers and topological entanglement between chains (i.e., two chains cannot pass through each other). If any other bond vectors were added to this set, some chains would become "phantom" chains.
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H/T)], where
H is the enthalpy change of the system. | RESULTS AND DISCUSSION |
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During the first stage, as shown in Fig. 2, the average hydropathy index of SRI using a window of 20 amino acids is calculated. To optimize the hydropathical interaction, the center of a transmembrane segment of 20 amino acids is located at those higher peaks of the hydropathy profile. Because no overlap is allowed for two segments, seven transmembrane segments are predicted for SRI from the first stage. The inset of Fig. 2 shows the reduction in hydrophobic energy when those transmembrane segments are placed in the membrane phase for various window sizes. The hydrophobic energy can be further reduced if the window size of each transmembrane segment is variable. This prediction is used to produce an initial configuration of SRI to perform MC simulations of its folding at the second stage: seven transmembrane segments are randomly distributed in the membrane phase, and two neighboring segments are connected by a random coil. The folding of the entire chain is simulated at this stage to optimize the enthalpy of the system. The result of the second stage is not sensitive to the window size used at the first stage. In fact, it remains the same even when only thirteen residues of each segment are placed in the membrane initially. Here we choose e1 = 0.3, e2 = 0, e3 = 0.3, e4 = 1.5, P = 0.1, and L = 23 lattice spacing (
31 Å, White and Wimley, 1999
). The choice of these parameters is not unique. Because all interactions in our model are weak forces, we expect these energetic parameters to be of the same order of magnitude (the strength of hydrogen bonding is taken to be of order 1). No drastic changes in the secondary structure of SRI are observed if a slightly different set of parameters is used. We note that, to obtain a better representation of
helices, the values of bending rigidity and lateral pressure adopted here are different from those in our previous study (Chen, 2001
). However the general features of folding dynamics and structure in this case are not affected. During this stage, the vdW interaction is switched off and the secondary structure formation is dominated by the hydrogen bonding and the hydropathical interaction. In Fig. 3, we show the comparison of the PDB secondary structure of SRI (A) (Berman et al., 2000
) to our predicted structures for L = 23 (B) and L = 24 (C). Both simulations predict a seven-helix structure of SRI. The average helix length of SRI is 22.4 aa in the PDB structure, and is 22.3 aa for L = 23 and 25.9 aa for L = 24. For L = 23, the prediction error in the average helix length is 0.6%, and the secondary structure alignment error (mismatch between Fig. 3 A and 3 B) is 11.3%. When the membrane thickness varies slightly, the seven-helix structure of SRI is still stable, but the helix regions will change correspondingly. For L = 24, its deviation from the PDB structure is 15.3% in the average helix length and is 17.6% in their mismatch. After the formation of all autonomous folding domains, we switch on the vdW interaction and switch off all other interactions. During this association stage, the initial configuration of SRI is taken from results at the second stage and each helix can only diffuse within the membrane (neighboring helices are constrained by their connecting loop). Packing of helices is a result of the vdW interaction alone. The external work done by the effective lateral pressure in our model does not drive helices to pack, because the helical structure (or projected area) of each transmembrane segment is fixed at this stage. Fig. 4 shows a comparison of our predicted tertiary structure (A) (only helical regions are shown) with the PDB structure (B). The resemblance of these two structures demonstrates the validity of our model in predicting the native structure of MPs. We note that tilting and distortion of transmembrane helices can be better studied in an off-lattice model, and the results will appear elsewhere (Chen and Chen, in preparation). Such a coarse-grained structure can be used as the initial configuration in an all-atom simulation or minimization to obtain a good native structure.
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-helix formation. As indicated from the Ramanchandran plot, the formation of idealized helices strongly depends on the backbone structures (Mathews and van Holde, 1996
-helix formation, which has been studied by both experiments and simulations (Deber and Li, 1995
4, our previous model has no cooperative effect and leads to an exponential growth of the folding time for helix formation as the helix length increases. To properly include the cooperative effect of (i, i ± 4) hydrogen bonding, here we add an extra favorable factor exp(
h) in the moving probability of each residue to enhance the cooperative helix formation, where
h is the change of (i, i ± 4) hydrogen bonding pairs and
is the cooperative factor. This cooperative effect on the folding time of a single transmembrane helix (AVATAYLGGAVALIVGVAFVWLLY, a transmembrane helix of SRI) has been studied for both random folding (with a random initial configuration) and assisted folding (with a parallel initial configuration to the membrane normal) using e1 = 0.3, e2 = 0, e3 = 0.3, e4 = 1.5, P = 0.1, T = 0.31 (the optimal folding temperature), and L = 24. The assisted folding is to mimic the helix formation of a hydrophobic segment assisted by a hydrophilic channel. This particular initial configuration selects a folding pathway with a smaller activated energy barrier than a random initial configuration, as described in our previous work (Chen, 2001
1.2 for both cases, as shown in Fig. 5. The folding time to a helical state increases exponentially if
deviates from this optimized value. For smaller values of
, the chain is easily trapped at wrongly folded states. If
is too large, the partially folded helix is often trapped at wrong positions in the membrane and the helix formation cannot continue to the rest of the peptide chain due to the presence of the water-membrane interface. These misfolded structures of a frustrated partial helix must be unfolded first before the chain can reach its ground state, which drastically increases the folding time. Note that, however, we do not know whether
is optimized for membrane protein folding or, if it is optimized, why.
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22. The initial drop in the MFPT of anchored chains is due to the fact that shorter chains have a smaller cooperative effect and thus they might take longer times to fold even when their configuration space is also smaller. Because anchored chains have a smaller configuration space and a larger cooperative effect than free chains, a smaller slope of the MFPT is observed for anchored chains. We note that anchored chains have a larger MFPT than free chains at short chain lengths due to the anchored restriction in their folding pathways.
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| CONCLUSIONS |
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h) to
-helical states. We find that the folding time of transmembrane helices is optimized for
= 1.2. The polypeptide chains are usually trapped at wrong configurations for small values of cooperativity, whereas they tend to be trapped at wrong positions in the membrane at large cooperativity. The dependence of folding time on chain length is nearly linear for free chains but exhibits an unusual behavior for anchored chains, which might result from the competition between cooperativity and the number of configurations as chain length varies. | ACKNOWLEDGEMENTS |
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This work is supported, in part, by the National Science Council of Taiwan under grant no. NSC 90-2112-M-003-024. C.M.C. is grateful for the hospitality at the Department of Pharmaceutical Chemistry, University of California at San Francisco.
Submitted on August 23, 2002; accepted for publication October 31, 2002.
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