Cheung Margaret S, Thirumalai D
Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
J Mol Biol. 2006 Mar 24;357(2):632-43. doi: 10.1016/j.jmb.2005.12.048. Epub 2006 Jan 5.
We have studied the stability and the yield of the folded WW domains in a spherical nanopore to provide insights into the changes in the folding characteristics due to interactions of the polypeptide (SP) with the walls of the pore. Using different models for the interactions between the nanopore and the polypeptide chain we have obtained results that are relevant to a broad range of experiments. (a) In the temperature and the strength of the SP-pore interaction plane (lambda), there are four "phases," namely, the unfolded state, the native state, the molten globule phase (MG), and the surface interaction-stabilized (SIS) state. The MG and SIS states are populated at moderate and large values of lambda, respectively. For a fixed pore size, the folding rates vary non-monotonically as lambda is varied with a maximum at lambda approximately 1 at which the SP-nanopore interaction is comparable to the stability of the native state. At large lambda values, the WW domain is kinetically trapped in the SIS states. Using multiple sequence alignment, we conclude that similar folding mechanism should be observed in other WW domains as well. (b) To mimic the changes in the nature of the allosterically driven SP-GroEL interactions we consider two models for the dynamic Anfinsen cage (DAC). In DAC1, the SP-cavity interaction cycles between hydrophobic (lambda>0) and hydrophilic (lambda=0) with a period tau. The yield of the native state is a maximum for an optimum value of tau=tau(OPT). At tau=tau(OPT), the largest yield of the native state is obtained when tau(H) approximately tau(P) where tau(H)(tau(P)) is the duration for which the cavity is hydrophobic (hydrophilic). Thus, in order to enhance the native state yield, the cycling rate, for a given loading rate of the GroEL nanomachine, should be maximized. In DAC2, the volume of the cavity is doubled (as happens when ATP and GroES bind to GroEL) and the SP-pore interaction simultaneously changes from hydrophobic to hydrophilic. In this case, we find greater increase in yield of the native state compared to DAC1 at all values of tau.
我们研究了球形纳米孔中折叠的WW结构域的稳定性和产率，以深入了解由于多肽（SP）与孔壁相互作用而导致的折叠特性变化。使用纳米孔与多肽链之间相互作用的不同模型，我们获得了与广泛实验相关的结果。（a）在温度和SP-孔相互作用强度平面（λ）中，存在四个“相”，即未折叠状态、天然状态、熔球态（MG）和表面相互作用稳定（SIS）状态。MG和SIS状态分别在中等和较大的λ值时出现。对于固定的孔径，随着λ的变化，折叠速率呈非单调变化，在λ约为1时达到最大值，此时SP-纳米孔相互作用与天然状态的稳定性相当。在大λ值时，WW结构域在动力学上被困在SIS状态。通过多序列比对，我们得出结论，在其他WW结构域中也应观察到类似的折叠机制。（b）为了模拟变构驱动的SP-GroEL相互作用性质的变化，我们考虑了两种动态安芬森笼（DAC）模型。在DAC1中，SP-腔相互作用在疏水（λ>0）和亲水（λ=0）之间以周期τ循环。天然状态的产率在τ=τ(OPT)的最佳值时最大。在τ=τ(OPT)时，当τ(H)约等于τ(P)时可获得最大的天然状态产率，其中τ(H)(τ(P))是腔为疏水（亲水）的持续时间。因此，为了提高天然状态产率，对于给定的GroEL纳米机器加载速率，循环速率应最大化。在DAC2中，腔的体积加倍（如ATP和GroES与GroEL结合时发生的情况），并且SP-孔相互作用同时从疏水变为亲水。在这种情况下，我们发现在所有τ值下，与DAC1相比，天然状态产率的增加更大。
