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首页> 外文期刊>Journal of Molecular Biology >Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins.
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Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins.

机译：螺旋-螺旋堆积和膜蛋白中残基的界面成对相互作用。

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Helix-helix packing plays a critical role in maintaining the tertiary structures of helical membrane proteins. By examining the overall distribution of voids and pockets in the transmembrane (TM) regions of helical membrane proteins, we found that bacteriorhodopsin and halorhodopsin are the most tightly packed, whereas mechanosensitive channel is the least tightly packed. Large residues F, W, and H have the highest propensity to be in a TM void or a pocket, whereas small residues such as S, G, A, and T are least likely to be found in a void or a pocket. The coordination number for non-bonded interactions for each of the residue types is found to correlate with the size of the residue. To assess specific interhelical interactions between residues, we have developed a new computational method to characterize nearest neighboring atoms that are in physical contact. Using an atom-based probabilistic model, we estimate the membrane helical interfacial pairwise (MHIP) propensity. We found that there are many residue pairs that have high propensity for interhelical interactions, but disulfide bonds are rarely found in the TM regions. The high propensity pairs include residue pairs between an aromatic residue and a basic residue (W-R, W-H, and Y-K). In addition, many residue pairs have high propensity to form interhelical polar-polar atomic contacts, for example, residue pairs between two ionizable residues, between one ionizable residue and one N or Q. Soluble proteins do not share this pattern of diverse polar-polar interhelical interaction. Exploratory analysis by clustering of the MHIP values suggests that residues similar in side-chain branchness, cyclic structures, and size tend to have correlated behavior in participating interhelical interactions. A chi-square test rejects the null hypothesis that membrane protein and soluble protein have the same distribution of interhelical pairwise propensity. This observation may help us to understand the folding mechanism of membrane proteins. Copyright 2001 Academic Press.
机译：螺旋-螺旋堆积在维持螺旋膜蛋白的三级结构中起关键作用。通过检查螺旋膜蛋白跨膜（TM）区域中空隙和囊袋的总体分布，我们发现细菌视紫红质和卤代视紫红质包装最紧密，而机械敏感通道包装最不紧密。大残基F，W和H在TM空隙或袋中的可能性最高，而小残渣（如S，G，A和T）在空隙或袋中的可能性最小。发现每种残基类型的非键相互作用的配位数与残基的大小相关。为了评估残基之间的特定螺旋间相互作用，我们开发了一种新的计算方法来表征物理接触中最邻近的原子。使用基于原子的概率模型，我们估计膜螺旋界面成对（MHIP）的倾向。我们发现有许多残基对具有极高的螺旋间相互作用倾向，但在TM区域中很少发现二硫键。高倾向对包括芳族残基和碱性残基（W-R，W-H和Y-K）之间的残基对。此外，许多残基对极易形成螺旋间的极性极性原子接触，例如，两个可电离的残基之间，一个可电离的残基与一个N或Q之间的残基对。可溶性蛋白质不具有这种多样的极性-极性模式螺旋间的相互作用。通过对MHIP值进行聚类的探索性分析表明，侧链分支，环状结构和大小相似的残基在参与的螺旋间相互作用中往往具有相关的行为。卡方检验否定了膜蛋白和可溶性蛋白具有相同的螺旋间成对倾向分布的零假设。该观察结果可以帮助我们理解膜蛋白的折叠机制。版权所有2001学术出版社。

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