Abstract The mitochondrial chaperone and co-chaperone HSP60/HSP10 (HSPD1/ HSPE1), the mammalian homologues of bacterial GroEL/GroES, form a barrel-and-lid complex to fold newly imported or misfolded mitochondrial proteins. Several lines of evidence suggest that HSPD1 and HSPE1 have diverged in function. HSPD1 and HSPE1...
ABSTRACT Background Glioblastoma (GBM) is the most aggressive form of primary brain cancer. Blood platelets have emerged as biomarkers where their RNA expression pattern indicates a tumor's presence. Our study aimed to characterize these patterns to identify biological processes associated with GBM and to evaluate thei...
Anna Giczewska, K. Pastuszak, L. van Hout et al.· Cancer Reports· 0 citations
Abstract Huntington's disease is caused by the trinucleotide repeat CAG expansion in the huntingtin gene, resulting in an N-terminal polyglutamine (polyQ) tract that renders the huntingtin protein (HTT) prone to misfolding and aggregation. Although polyQ expansion is an intrinsic driver of aggregation, the folding traj...
Abstract Cells survive and reproduce by coping with acute or chronic exposure to a fixed elevated temperature or fluctuating temperatures. These properties are one of the main evolutionary forces and involve the heat shock response. This response is characterized by the induction of heat-shock proteins (HSPs) and is ma...
In vivo function of Caenorhabditis elegans HSP-12.6 is examined, finding that HSP-12.6 exhibits exceptional selectivity in protecting the muscle function against folding or assembly mutations in thick filament proteins, but not in thin filament or non-filament proteins.
Abigail Fern, J. Alexander-Floyd, Anhelina Volchok et al.· Philosophical transactions o...· 0 citations
Many applications in statistics, economics, and physics require sampling from high-dimensional categorical distributions with local dependence structures. Examples include finite memory language models, Ising and Potts systems in statistical physics and protein folding, etc. In modern machine learning, discrete diffusi...
The generalized Schr\"odinger bridge on a graph moves mass between two distributions while charging a cost for the states visited. It has been approached by learning the rates of a controlled continuous-time Markov chain, with a temporal-difference penalty that restores the cost. A state cost folds into the reference p...
Intrinsically disordered protein regions (IDRs) play central roles in cellular processes such as transcriptional regulation, signal transduction, and subcellular localization, yet their functional design remains challenging. Structure-based design methods do not readily apply to IDRs, and existing protein language mode...
J. Liu, Sebastian Ibarraran, Frank Hu et al.· 0 citations
Cryptic ligand-binding pockets are not apparent in experimentally determined apo structures, making them difficult to identify from unbound receptor geometry. A complementary challenge is to make the structural measurements and learned evidence behind each prediction directly inspectable. We introduce a supervised alge...
The central challenge in de novo protein design is generating plausible, mutually compatible structures and sequences, such that each designed sequence folds into its intended structure and the structure accommodates that sequence. Compared to typical two-stage design methods, which decouple the modeling of the interde...
Yuan-Le Mo, Bo Qiang, Hai-Tao Lin et al.· 0 citations
Infection with human immunodeficiency virus (HIV) is currently incurable because the virus integrates into the host genome of long-lived memory CD4+ T cells and can persist in a transcriptionally silent state, known as latency. Antiretroviral therapy (ART) effectively suppresses viral replication, restores CD4+ T cell...
This biomarker panel covers three core pathological processes-atherosclerosis and vascular calcification, chronic inflammation, and hypercoagulable state-providing candidate biomarkers that warrant further investigation for disease-state characterization and risk stratification, particularly in high-latitude cold-regio...
Ning-Ning Wang, Zheng-Guang Guo, Ming Jin et al.· Frontiers in Neurology· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
