Raymond James A
School of Life Sciences, University of Nevada Las Vegas, Las Vegas, USA.
Extremophiles. 2024 Dec 13;29(1):8. doi: 10.1007/s00792-024-01374-y.
Among the many ice-binding proteins (IBPs) found in microorganisms (bacteria, archaea, fungi and algae), the canonical DUF3494 beta-barrel type is the most common. Until now, little variation has been found in this structure: an initial coil leads into an alpha helix that directs the following coils into a reverse stack, with the final coil ending up next to the initial coil. Here, I show that there exist many bacterial proteins whose AlphaFold-predicted structures deviate from the DUF3494 structure so that they are not recognized as belonging to an existing DUF or Pfam family. In these non-canonical DUF3494 (ncDUF3494) proteins, the number of coils in the alpha helix is highly variable, often being as high as 14. The putative ice-binding sides of each of 13 proteins modeled have a well-aligned row of hydrophilic residues, with spacings that are close to the repeat distance on the ice a-axis. A recombinant protein made for one of the proteins showed that it had ice-binding activity, even in the µg/ml range. The ncDUF3494 proteins appear to be found only in bacteria, the great majority of which live in icy habitats. C-terminal PEP-Cterm motifs, which are rare in DUF3494s, are present in most of the ncDUF3494s, possibly indicating a secretory function. The relatively narrow distribution of ncDUF3494 proteins suggests that they are a later development in DUF3494 evolution.
在微生物（细菌、古菌、真菌和藻类）中发现的众多冰结合蛋白（IBP）中，典型的DUF3494β桶型是最常见的。到目前为止，在这种结构中发现的变异很少：最初的线圈会引导至一个α螺旋，该螺旋将后续的线圈导向反向堆叠，最终的线圈会在最初的线圈旁边结束。在这里，我表明存在许多细菌蛋白，其AlphaFold预测的结构与DUF3494结构不同，因此它们不被认为属于现有的DUF或Pfam家族。在这些非典型DUF3494（ncDUF3494）蛋白中，α螺旋中的线圈数量高度可变，通常高达14个。所建模的13种蛋白质中每种蛋白质的假定冰结合面都有一排排列良好的亲水残基，其间距接近冰a轴上的重复距离。为其中一种蛋白质制备的重组蛋白表明，即使在微克/毫升范围内，它也具有冰结合活性。ncDUF3494蛋白似乎仅在细菌中发现，其中绝大多数生活在冰冷的栖息地。在大多数ncDUF3494蛋白中存在DUF3494中罕见的C末端PEP-Cterm基序，这可能表明其具有分泌功能。ncDUF3494蛋白相对狭窄的分布表明它们是DUF3494进化中的后期发展产物。
