Exploring the multi-dimensional energy landscape of a large protein in detail is a computational challenge. Such investigations may include analysis of multiple folding pathways, rate constants for important conformational transitions, locating intermediate states populated during folding, estimating energetic and entropic barriers that separate populated basins, and visualising a high-dimensional surface. The complexity of the landscape can be simplified through coarse-grained structure-based models (SBMs). These widely used coarse-grained representations of proteins provide a minimalist approximation to the free energy landscape, which subsumes the folding behaviour of many single-domain proteins. Here we describe the combination of SBMs with discrete path sampling (DPS), and show how this approach can provide details of the landscape and folding pathways. Combining SBMs and DPS provides an efficient framework for sampling the protein free energy landscape and for calculating various kinetic and thermodynamic quantities.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.sbi.2020.07.003 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Mapping species of greatest conservation need and solar energy potential in the arid Southwest for future sustainable development.
PeerJ
January 2025
School of Applied Sciences and Arts, College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States of America.
The need for renewable energy has become increasingly evident in response to the climate change crisis, presenting a paradoxical challenge to biodiversity conservation. The Southwest United States is desirable for large-scale solar energy development (SED) due to its high global horizontal irradiance (GHI) values and vast open landscapes. However, this region is also rich in unique ecological and biological diversity.
View Article and Find Full Text PDFFreestanding Wide-Bandgap Semiconductors Nanomembrane from 2D to 3D Materials and Their Applications.
Small Methods
January 2025
Wide-bandgap semiconductors (WBGS) with energy bandgaps larger than 3.4 eV for GaN and 3.2 eV for SiC have gained attention for their superior electrical and thermal properties, which enable high-power, high-frequency, and harsh-environment devices beyond the capabilities of conventional semiconductors.
View Article and Find Full Text PDFMolecular interaction profiling and binding dynamics of Cinnamomum zeylanicum phytochemicals with human pancreatic amylase.
J Mol Graph Model
January 2025
Department of Biotechnology, PES University, Bengaluru 560085, India.
Diabetes mellitus, characterized by persistent hyperglycemia, remains a critical global health challenge. Inhibition of human pancreatic alpha-amylase, a key enzyme catalyzing carbohydrate digestion, is a promising approach to manage postprandial glucose levels. Cinnamomum zeylanicum, a medicinal plant known for its therapeutic potential, harbors bioactive compounds that can act as natural alpha-amylase inhibitors, though their mechanisms remain underexplored.
View Article and Find Full Text PDFProton Accumulation Modulated Surface Potential in Proton Conducting Ceramics Revealed by Near-Ambient Pressure X-ray Photoelectron Spectroscopy.
ACS Appl Mater Interfaces
January 2025
University of Michigan - Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai 200240, China.
Proton conducting electrochemical cells (PCECs) are efficient and clean intermediate-temperature energy conversion devices. The proton concentration across the PCECs is often nonuniform, and characterizing the distribution of proton concentration can help to locate the position of rate-limiting reactions. However, the determination of the local proton concentration under operating conditions remains challenging.
View Article and Find Full Text PDFDesigning highly tunable nanostructured peptide hydrogels using differential thermal histories to achieve variable cellular responses.
Nanoscale
January 2025
Institute of Nano Science and Technology, Mohali, Sector-81, Knowledge City, Sahibzada Ajit Singh Nagar, Punjab 140306, India.
In this study, we demonstrate a unique and promising approach to access peptide-based diverse nanostructures in a single gelator regime that is capable of exhibiting different surface topographies and variable physical properties, which, in turn, can effectively mimic the extracellular matrix (ECM) and regulate variable cellular responses. These diverse nanostructures represent different energy states in the free energy landscape, which have been created through different self-assembling pathways by providing variable energy inputs by simply altering the gelation induction temperature from 40 °C to 90 °C. The highly entangled network structure with long fibers was created by higher energy inputs, , inducing the gelation at a higher temperature in the 70-90 °C range, whereas the less entangled nanoscale network with short fibers was obtained at a lower gelation induction temperature of 40-60 °C.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!