Biology subjects

Xu, S. Y.

Publications and source records attributed to Xu, S. Y..

3 recordsLinked to original sources

bioRxiv2026

Sequence-dependent Stability and the Apparent Two-state Thermal Transition of Extended Collagen Triple Helices

The thermal stability of collagen triple helices is strongly influenced by the amino acid sequence of the repeating Gly-X-Y tripeptides, yet how these residue-specific interactions are integrated within an extended triple helix to determine thermal behavior remains poorly understood. Here, we addressed this question using recombinant collagen mimetic peptides (rCMPs) containing extended native sequences from the 1(I) and 2(I) chains of human type I collagen. Triple-helix formation was nucleated by a C-terminal foldon domain and further stabilized by interchain disulfide crosslinking, allowing the apparent melting temperature (T) to reflect interactions within the triple-helical domain independent of nucleation. The stabilizing effects of Pro and Y-position Arg identified in host-guest peptides were largely preserved in extended triple helices, whereas the proposed Lys-Gly-Glu (KGE) interchain salt bridge produced little measurable stabilization, demonstrating the influence of sequence context. Remarkably, identical triple-helical sequences exhibited markedly different thermal behavior when unfolding was initiated under different conditions. Nevertheless, extended triple helices differing substantially in sequence and length retained an apparently two-state thermal transition. These findings support a mechanism in which unfolding is preferentially initiated within regions of lower intrinsic stability, while the continuity of the triple helix couples neighboring regions into a cooperative unfolding process throughout the helix. This mechanism provides a plausible explanation for the longstanding paradox that extended collagen triple helices exhibit persistent sequence-dependent thermodynamic heterogeneity despite a two-state thermal transition, and a framework for investigating how sequence-dependent stability contributes to the structure and function of collagen molecules. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/741348v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@64f65borg.highwire.dtl.DTLVardef@69f999org.highwire.dtl.DTLVardef@181b647org.highwire.dtl.DTLVardef@e60ccf_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Prevalence of errors in lab-made plasmids across the globe

Plasmids are indispensable in life sciences research and therapeutics development. Currently, most labs custom-build their plasmids. As yet, no systematic data on the quality of lab-made plasmids exist. Here, we report a broad survey of plasmids from hundreds of academic and industrial labs worldwide. We show that nearly half of them contained design and/or sequence errors. For transfer plasmids used in making AAV vectors, which are widely used in gene therapy, about 40% carried mutations in the inverted terminal repeat (ITR) regions due to their inherent instability, which is influenced by flanking GC content. We also list genes difficult to clone into plasmid or package into virus due to their toxicity. Our finding raises serious concerns over the trustworthiness of lab-made plasmids, which parallels the underappreciated mycoplasma contamination and misidentified mammalian cell lines reported previously, and highlights the need for community-wide standards to uphold the quality of this ubiquitous reagent in research and medicine. Accordingly, we propose the concept of good vector practice (GVP) that covers the proper design, construction, in-process QC, final QC, banking and management of plasmids in research and medicine to uphold their quality.

molecular biology↗

bioRxiv2022

Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor

Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multi-valent interactions to form stable complexes that are simultaneously capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multi-site competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo; an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to be the first of many that use DNA origami structures to exploit multi-valent interactions for the design and synthesis of a wide range of possible kinetic behaviors.

synthetic biology↗