Computational protein design has emerged as a powerful tool capable of identifying sequences compatible with pre-defined protein structures. The sequence design protocols, implemented in the Rosetta suite, have become widely used in the protein engineering community. To understand the strengths and limitations of the Rosetta design framework, we tested several design protocols on two distinct folds (SH3-1 and Ubiquitin). The sequence optimization, when started from native structures and natural sequences or polyvaline sequences, converges to sequences that are not recognized as belonging to the fold family of the target protein by standard bioinformatic tools, such as BLAST and Hmmer. The sequences generated from both starting conditions (native and polyvaline) are instead very similar to each other and recognized by Hmmer as belonging to the same "family." This demonstrates the capability of Rosetta to converge to similar sequences, even when sampling from distinct starting conditions, but, on the other hand, shows intrinsic inaccuracy of the scoring function that drifts toward sequences that lack identifiable natural sequence signatures. To address this problem, we developed a protocol embedding Rosetta Design simulations in a genetic algorithm, in which the sequence search is biased to converge to sequences that exist in nature. This protocol allows us to obtain sequences that have recognizable natural sequence signatures and, experimentally, the designed proteins are biochemically well behaved and thermodynamically stable.
Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States.
DNA interstrand cross-links (ICLs) are the sources of the cytotoxicity of many anticancer agents. Selenium compounds showed great potential as anticancer drugs. In this work, we synthesized a binaphthalene analog containing phenyl selenide (-SePh) as the leaving group and investigated its photochemical reactivity toward DNA as well as its cytotoxicity and selectivity.
Background: Sarcomatoid carcinomas (SC) are rare tumors with both epithelial and mesenchymal characteristics, linked to aggressive behavior and poor prognosis. Sarcomatoid carcinoma of unknown primary (SCUP) is an exceedingly rare subset with limited literature and no standardized management guidelines. This study aims to characterize the clinical presentations, treatment patterns, and genomic landscape of SCUP.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan 475004, P.R. China. Electronic address:
Gossypium spp. pigment glands are a good model for studying plant secretory cavity structures. GoPGF (GOSSYPIUM PIGMENT GLAND FORMATION) is a well-characterized master transcription factor that controls gland formation in cotton; however, little is known about its transcriptional regulation.
Macrophage efferocytosis (clearance of apoptotic cells) is crucial for tissue homeostasis and wound repair, where macrophages secrete factors that promote resolution of inflammation and regenerative signalling. This study examined the role of efferocytic macrophage-associated CCL2 secretion, its influence on mesenchymal stem/progenitor cell (MSPC) chemotaxis, and in vivo cell recruitment using Ccr2 (KO) mice with disrupted CCL2 receptor signalling in two regenerative models: ossicle implants and ulnar stress fractures. Single cell RNA sequencing and PCR validation indicated that efferocytosis of various apoptotic cells at bone injury sites (osteoblasts, pre-osteoblasts, MSPC) upregulated CCL2.
