Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a “spatial motif” and several “fold specific hot spots” that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.氨基酸序列所编码的折叠通路保真度，在以下情形中面临挑战：无序列同源性、执行不同功能且无明显进化关联的蛋白质，却采用了相似的折叠构象。反之，该问题的另一面是：多样化的序列集合所能利用的折叠空间十分有限。核心问题在于，哪些因素促使多样化序列形成特定的折叠构象。本研究以结合烟酰胺腺嘌呤二核苷酸（NAD）与烟酰胺腺嘌呤二核苷酸磷酸（NADP）的罗斯曼折叠（Rossmann fold）结构域为研究案例，借助网络理论相关概念，揭示了驱动该折叠构象形成的共有结构特征。我们提出了一种图论形式化方法，用以从全局结构环境下的保守原子相互作用角度捕捉结构细节，进而从多样化序列中提取核心拓扑特征。通过将不同结构统一为统一的数学表征，并结合若干网络参数的精心组合，我们得以探究驱动蛋白质采用NAD(P)结合罗斯曼折叠构象的结构特征。相较于参与这些相互作用的氨基酸残基，关键位置的原子相互作用在蛋白质中似乎更为保守。我们提出了一种“空间基序”以及若干“折叠特异性热点位点”，它们共同构成了NAD(P)结合罗斯曼折叠结构域的标志性结构蓝图。本研究结果与此前的实验及理论研究高度吻合，验证了该方法的稳健性与有效性。此外，将本研究结果与统计耦合分析（SCA）进行对比，进一步为该方法提供了支撑。本文提出的方法具有普适性，可应用于其他类似的相关研究问题。