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首页> 外文期刊>The Journal of Chemical Physics >Combinatorial design of protein sequences with applicationsto lattice and real proteins
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Combinatorial design of protein sequences with applicationsto lattice and real proteins

机译：蛋白质序列的组合设计及其在晶格和真实蛋白质中的应用

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摘要

Understanding the evolution of protein structures from specific sequences may be achieved bypredicting the desired folded structure from a given sequence and by predicting compatiblesequences from a known structure using principles of protein folding and design. Protein designrequires the synthesis of a broad range of sequences consistent with a preassigned targetconformation. However, the number of possible protein sequences for a given target structureexponentially increases with the number of residues making the explicit tabulation of all sequencesintractable experimentally and computationally. For sequence libraries of arbitrary size, the resultsof a self-consistent mean field theory is applied to a three-dimensional cubic lattice model ofproteins and real homologous protein sequences to estimate the number and probabilisticcomposition of sequences consistent with a generalized foldability criterion. Theoreticallycalculated site-specific monomer probabilities and the monomer pair probabilities at each positionin a sequence are compared to those obtained from exact enumeration for cubic lattice proteins. Forreal proteins the theoretically predicted sequence variability are compared to that obtained from a setof homologous protein sequences. The theory results match extremely well with both the cubiclattice protein and real protein results. The theory also evaluates the mutability of specific residuesand identifies the beneficial mutations. The theory may be used to quantify particular designstrategies and explore site-directed mutagenesis strategies in crafting de novo proteins in context ofin vitro protein evolution.
机译：通过从给定序列中预测所需的折叠结构，并通过使用蛋白质折叠和设计原理从已知结构中预测相容序列，可以实现从特定序列中了解蛋白质结构的进化。蛋白质设计需要合成与预定的靶标构象一致的广泛序列。然而，给定靶结构的可能蛋白质序列的数目随残基的数目呈指数增加，这使得所有序列的显式列表在实验和计算上都难以实现。对于任意大小的序列文库，将自洽平均场理论的结果应用于蛋白质和真实同源蛋白质序列的三维立方晶格模型，以估计符合广义可折叠性标准的序列数和概率组成。将理论计算的位点特异性单体概率和序列中每个位置的单体对概率与从精确枚举的立方晶格蛋白质获得的概率进行比较。对于真实蛋白质，将理论上预测的序列变异性与从一组同源蛋白质序列获得的变异性进行比较。理论结果与立方晶格蛋白质和真实蛋白质的结果非常匹配。该理论还评估了特定残基的变异性，并确定了有益的突变。该理论可用于量化特定的设计策略，并探索在体外蛋白质进化过程中从头构建蛋白质的定点诱变策略。

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