标题： 立体化学约束对折叠蛋白质结构特性的影响 显示英文标题

标题： The effect of stereochemical constraints on the structural properties of folded proteins

摘要： 蛋白质由折叠成复杂三维结构的氨基酸链组成。 几个关键特征，如回转半径、核心氨基酸的比例$f_{\rm core}$，核心氨基酸的堆积分数$\langle \phi\rangle$以及结构因子$S(q)$定义了折叠蛋白质的结构。 众所周知，折叠的蛋白质是紧凑的，其回转半径$R_g(N) \sim N^{\nu}$遵循与氨基酸数目$N$和$\nu \sim 1/3$，$f_{\rm core} \approx 0.09$，和$\langle \phi \rangle \approx 0.55$的幂律缩放。 We also investigate the {\it 内部} scaling of the radius of gyration $R_g(n)$ versus the chemical separation $n$ between amino acids for subchains of length $n$ and show that it does not obey simple power-law scaling with $\nu \sim 1/3$. 相反，$R_g(n) \sim n^{\nu_{1,2}}$在小$n$时具有较大的指数$\nu_1 > 1/3$，而在大$n$时具有较小的指数$\nu_{2} < 1/3$。 为了开发一个能够再现这些定义结构特征的蛋白质最小模型，我们对一系列复杂度逐渐增加的粗粒度模型进行了坍缩模拟。 我们证明了一个模型，该模型将氨基酸粗粒化为一个单一的球形主链珠和几个大小可变的侧链珠，并对主链施加弯曲角和二面角约束，能够再现超过$2500$个蛋白质的X射线晶体结构中的$R_g(n)$、$f_{\rm core}$、$\langle \phi \rangle$和$S(q)$。 显示英文摘要

摘要： Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids $f_{\rm core}$, packing fraction $\langle \phi\rangle$ of core amino acids, and structure factor $S(q)$ define the structure of folded proteins. It is well-known that folded proteins are compact with a radius of gyration $R_g(N) \sim N^{\nu}$ that obeys power-law scaling with the number of amino acids $N$ and $\nu \sim 1/3$, $f_{\rm core} \approx 0.09$, and $\langle \phi \rangle \approx 0.55$. We also investigate the {\it internal} scaling of the radius of gyration $R_g(n)$ versus the chemical separation $n$ between amino acids for subchains of length $n$ and show that it does not obey simple power-law scaling with $\nu \sim 1/3$. Instead, $R_g(n) \sim n^{\nu_{1,2}}$ with a larger exponent $\nu_1 > 1/3$ for small $n$ and smaller exponent $\nu_{2} < 1/3$ for large $n$. To develop a minimal model for proteins that recapitulates these defining structural features, we carry out collapse simulations for a series of coarse-grained models with increasing complexity. We show that a model, which coarse-grains amino acids into a single spherical backbone bead and several variable-sized side-chain beads and enforces bend- and dihedral-angle constraints for the backbone, recapitulates $R_g(n)$, $f_{\rm core}$, $\langle \phi \rangle$, and $S(q)$ for more than $2500$ x-ray crystal structures of proteins.