Publications by authors named "J R Sachleben"
Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.
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- * Researchers utilized hydrogen-deuterium exchange/mass spectrometry to explore how Pab1's structure changes under stress, revealing that its RNA recognition motifs (RRMs) partially unfold and interact differently depending on the type of stress.
- * The study identifies a process called sequential activation, where RRMs activate at specific temperatures, enabling Pab1 to form condensates through interactions driven by thermodynamic properties, highlighting a general mechanism for stress-response in proteins.
Article Synopsis
- Local changes in DNA base-pairing stability due to lesions and modifications can impact the entire oligonucleotide's stability and dynamics, often overlooked in research.
- The study focuses on how the position of an abasic site (AP site) affects the stability and dynamics of short DNA duplexes, using spectroscopy and molecular dynamics simulations to explore this relationship.
- Findings reveal that the position of the AP site creates an entropic barrier that influences base-pairing and fraying, with specific nucleobase sequences playing a crucial role in modulating this effect and impacting overall duplex stability.
Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes.
View Article and Find Full Text PDFHybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy.
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