The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide statistical evidence for the involvement of highly mobile and disordered regions in complex assembly. We ordered the entire set of X-ray crystallographic structures in the PDB into hierarchies of progressive interactions involving identical or very similar protein chains, yielding 40205 hierarchies of complexes with increasing numbers of partners. We then examine them as proxies for the assembly pathways. Using this database, we show that upon oligomerisation, new interfaces tend to be observed at residues that were characterised as softly disordered (flexible, amorphous or missing residues) in the complexes preceding them in the hierarchy. We also rule out the possibility that this correlation is just a surface effect by restricting the analysis to residues on the surface. Interestingly, we find that the location of soft disordered residues in the sequence changes as the number of partners increases. Our results show that there is a general mechanism for protein assembly that involves soft disorder and modulates the way protein complexes are assembled. This work highlights the difficulty of predicting the structure of large protein complexes from sequence and emphasises the importance of linking predictors of disorder to the next generation of predictors of complex structure. Finally, we investigate the relationship between the AF2's confidence metric pLDDT for structure prediction in unbound vs. bound structures, and soft disorder. We show a strong correlation between AF2 low confidence residues and the union of all regions of soft disorder observed in the hierarchy. This paves the way for using the pLDDT metric as a proxy for predicting assembly paths.
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific sequence of assembly steps. Using droplet interfaces to position compartment boundaries, we show that an assembly line can be self organized by active droplets. As a consequence, assembly steps can be arranged spatially so that a specific order of assembly is achieved and incorrect assembly is strongly suppressed.
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms. Here, we combine experiments and simulations to examine the folding/unfolding pathways of the VPK pseudoknot, a variant of the Mouse Mammary Tumor Virus (MMTV) PK involved in ribosomal frameshifting. Fluorescent nucleotide analogs (2-aminopurine and pyrrolocytidine) …
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered crystalline assemblies, and instead, disordered structures start to form when the chain length exceeds a certain threshold, which is consistent with the previous experiments. Further analysis of the simulation data suggests weakening interparticle interactions with increasing chain length, thereby shifting the suitable assembly conditions to lower temperatures …
Silk cocoons are reconstituted into an aqueous suspension, and protein stability is investigated by comparing the protein's response to hydrochloric acid and sodium chloride. Aggregation occurs at <8 mM hydrochloric acid that is not correlated to protein protonation, while sodium chloride over the same range of concentrations does not cause aggregation. We measure the structures present on the protein and aggregate lengthscales in these solutions using both optical and neutron scattering, while mass spectrometry techniques shed light on a possible mechanism for aggregate formation. We find tha…
Nature is remarkably adept at using interfaces to build structures, encapsulate reagents, and regulate biological processes. Inspired by Nature, we describe flexible polymer-based ribbons, termed "mesoscale polymers" (MSPs), to modulate interfacial interactions with liquid droplets. This produces unprecedented hybrid assemblies in the forms of flagellum-like structures and MSP-wrapped droplets. Successful preparation of these hybrid structures hinges on interfacial interactions and tailored MSP compositions, such as MSPs with domains possessing distinctly different affinity for fluid-fluid int…
Living cells dynamically modulate the local morphologies of their actin cytoskeletons to perform biological functions, including force transduction, intracellular transport, and cell division. A major challenge is to understand how diverse structures of the actin cytoskeleton are assembled from a limited set of molecular building blocks. Here we study the spontaneous self-assembly of a minimal model of cytoskeletal materials, consisting of semiflexible actin filaments, crosslinkers, and molecular motors. Using coarse-grained simulations, we demonstrate that by changing concentrations and kinet…
The biophysical analysis of dynamically formed multi-protein complexes in solution presents a formidable technical challenge. Sedimentation velocity (SV) analytical ultracentrifugation achieves strongly size-dependent hydrodynamic resolution of different size species, and can be combined with multi-component detection by exploiting different spectral properties or temporally modulated signals from photoswitchable proteins. Coexisting complexes arising from self- or hetero-associations that can be distinguished in SV allow measurement of their stoichiometry, affinity, and cooperativity. However…
Molecular simulation analysis of structural variations in lipoplexes
我们使用一个粗粒度的分子模型来研究阳离子和中性脂质与DNA分子的复合物（“lipoplexes”）的自组装过程-一种有前途的非病毒DNA载体用于基因治疗。我们通过直接可视化的分子排列和通过计算相应的散射图来确定所得到的结构。后一种方法提供了一种手段，从X射线散射实验与公布的数据进行比较。与实验结果一致，我们发现，在增加的脂质材料的刚度，系统往往形成层状结构。从层状复合物的散射图中可以提取两个特征距离-层状（层间）间距和每层内的DNA间距。我们发现这两个量的计算值与实验数据之间有很好的一致性[J.O.雷德勒岛Koltover，T. Salditt和C. R. Safinya，Science Vol.275，810（1997）]在实验研究的带电脂质（CL）的摩尔分数的整个范围内。对模拟系统的目视检查表明，对于非常高分数的CL，自发形成由结合到小膜片段的DNA分子组成的无序结构。这些非层状无序复合物的衍射图似乎非常相似的层状结构，这使得解释的X射线数据模糊。层状秩序的损失可能是所观察到的脂质复合物作为基因递送载体在高电荷密度下的效率增加的起源。
