Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme.

Nat Commun

Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden.

Published: May 2020

Cold-adapted enzymes from psychrophilic species show the general characteristics of being more heat labile, and having a different balance between enthalpic and entropic contributions to free energy barrier of the catalyzed reaction compared to mesophilic orthologs. Among cold-adapted enzymes, there are also examples that show an enigmatic inactivation at higher temperatures before unfolding of the protein occurs. Here, we analyze these phenomena by extensive computer simulations of the catalytic reactions of psychrophilic and mesophilic α-amylases. The calculations yield temperature dependent reaction rates in good agreement with experiment, and also elicit the anomalous rate optimum for the cold-adapted enzyme, which occurs about 15 °C below the melting point. This result allows us to examine the structural basis of thermal inactivation, which turns out to be caused by breaking of a specific enzyme-substrate interaction. This type of behaviour is also likely to be relevant for other enzymes displaying such anomalous temperature optima.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7250929PMC
http://dx.doi.org/10.1038/s41467-020-16341-2DOI Listing

Publication Analysis

Top Keywords

computer simulations
8
anomalous temperature
8
optimum cold-adapted
8
cold-adapted enzyme
8
cold-adapted enzymes
8
simulations explain
4
explain anomalous
4
temperature optimum
4
cold-adapted
4
enzyme cold-adapted
4

Similar Publications

Background Detection and segmentation of lung tumors on CT scans are critical for monitoring cancer progression, evaluating treatment responses, and planning radiation therapy; however, manual delineation is labor-intensive and subject to physician variability. Purpose To develop and evaluate an ensemble deep learning model for automating identification and segmentation of lung tumors on CT scans. Materials and Methods A retrospective study was conducted between July 2019 and November 2024 using a large dataset of CT simulation scans and clinical lung tumor segmentations from radiotherapy plans.

View Article and Find Full Text PDF

Thermal Titration Molecular Dynamics: The Revenge of the Fragments.

J Chem Inf Model

January 2025

Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.

During the last 20 years, the fragment-based drug discovery approach gained popularity in both industrial and academic settings due to its efficient exploration of the chemical space. This bottom-up approach relies on identifying high-efficiency small ligands (fragments) that bind to a target binding site and then rationally evolve them into mature druglike compounds. To achieve such a task, researchers rely on accurate information about the ligand binding mode, usually obtained through experimental techniques, such as X-ray crystallography or computer simulations.

View Article and Find Full Text PDF

In the era of big data, increasing availability of data makes combining different data sources to obtain more accurate estimations a popular topic. However, the development of data integration is often hindered by the heterogeneity in data forms across studies. In this paper, we focus on a case in survival analysis where we have primary study data with a continuous time-to-event outcome and complete covariate measurements, while the data from an external study contain an outcome observed at regular intervals, and only a subset of covariates is measured.

View Article and Find Full Text PDF

Background: The role of cancer-associated pericytes (CAPs) in tumor microenvironment (TME) suggests that they are potential targets for cancer treatment. The mechanism of CAP heterogeneity in esophageal squamous cell carcinoma (ESCC) remains unclear, which has limited the development of treatments for tumors through CAPs. Therefore, a comprehensive understanding of the classification, function, cellular communication and spatial distribution of CAP subpopulations in ESCC is urgently needed.

View Article and Find Full Text PDF

Background: Cerebral palsy (CP) is a neurological disorder that can affect motor skills and psychophysiological well-being. Virtual Reality Exercise (VRE) improves cognitive and physical outcomes in patients with CP. Therefore, this study aimed to investigate the effects of VRE on attention, vigor, and decision-making abilities in adolescents with CP.

View Article and Find Full Text PDF

Want 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!