Biology subjects

Mariano, N.

Publications and source records attributed to Mariano, N..

3 recordsLinked to original sources

bioRxiv2026

A recombinant heterotrimeric mini-procollagen I reveals new functional and structural roles for the α2(I) chain

Collagen I provides mechanical stability to organs and plays a critical role in several physiological processes such as wound healing and bone remodeling. Its ability to form fibrils depends on the proteolytic conversion of soluble procollagen I into mature protomers. However, the mechanistic aspects of this critical step have been difficult to analyze due to the lack of recombinant procollagen I suitable for structural and biochemical analyses. Here, we describe the successful production and purification of a heterotrimeric mini-procollagen I [1(I)22(I)] together with its homotrimeric counterpart [1(I)3] in HEK293-F cells. These tools were used to probe the specific role of the 2(I) chain both in procollagen I assembly and proteolytic maturation. While the presence of 2(I) in the heterotrimer does not strengthen trimer interfaces on its own, as revealed by cryo-electron microscopy, it provides a clear functional advantage to the procollagen substrate that is cleaved more efficiently by bone morphogenetic protein 1 (BMP-1) than the homotrimer. Furthermore, we demonstrate that the first cleavage event in the heterotrimer is at the level of the 2(I) chain, through a mechanism involving its C-telopeptide and a specific PRS motif close to the cleavage site. The preferential cleavage of 2(I) by BMP-1 can be partially corrected in the presence of PCPE-1 (procollagen C-proteinase enhancer 1) but the efficacy of the correction depends on its position on the procollagen trimer. Finally, we solved the high-resolution structure of the complex between the heterotrimer and PCPE-1 and proposed a new mechanism to explain the enhancing activity of PCPE-1.

biochemistry↗

bioRxiv2024

Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip

As genome sequencing technologies advance, the accumulation of sequencing data in public databases necessitates more robust and adaptable data analysis workflows. Here, we present Rocketchip, which aims to offer a solution to this problem by allowing researchers to easily compare and swap out different components of ChIP-seq, CUT&RUN, and CUT&Tag data analysis, thereby facilitating the identification of reliable analysis methodologies. Rocketchip enables researchers to efficiently process large datasets while ensuring reproducibility and allowing for the reanalysis of existing data. By supporting comparative analyses across different datasets and methodologies, Rocketchip contributes to the rigor and reproducibility of scientific findings. Furthermore, Rocketchip serves as a platform for benchmarking algorithms, allowing researchers to identify the most accurate and efficient analytical approaches to be applied to their data. In emphasizing reproducibility and adaptability, Rocketchip represents a significant step towards fostering robust scientific research practices.

bioinformatics↗

bioRxiv2022

Production of recombinant heterotrimeric mini-procollagen I and homotrimeric II mini-procollagen II reveals new cleavage sites for BMP-1

The proteolytic conversion of soluble procollagens into mature collagen monomers is a critical step to decrease their solubility and trigger collagen fibril formation. In the case of collagens I, II and III, this maturation process is driven by several extracellular metalloproteinases such as BMP-1, tolloid-like proteinases, meprin , meprin {beta}, ADAMTS-2 and ADAMTS-14 but the extensive characterization of these proteolytic events has been hampered by the lack of recombinant procollagens. We previously reported the production and partial characterization of recombinant homotrimeric proteins derived from procollagen III (mini-procollagens III) and, in this study, we describe how we have extended this previous work to the production of heterotrimeric mini-procollagen I and homotrimeric mini-procollagen II. These mini-procollagens include truncated triple helices and intact C-telopeptide and C-propeptide domains and were produced in suspension in HEK293-F cells with yields ranging from 2.5 mg/L to 10 mg/L after purification. They proved very useful tools to analyze the effect of calcium on the stability of the procollagen C-terminal region and to compare the procollagen C-proteinase activity of BMP-1 on the three major fibrillar procollagens or their ability to interact with various partners such as PCPE-1. Using mass spectrometry to map BMP-1 cleavage sites on the mini-procollagens, we confirmed all previously described sites but also revealed two additional cleavage sites in the 1 chain of procollagens I and II. This result shows that the mini-procollagen toolkit offers a broad range of perspectives to make functional studies but also possibly structural analyses or to develop drug screening assays.

biochemistry↗