Structural Properties of Rat Intestinal Fatty Acid-Binding Protein with its Dynamics: Insights into Intrinsic Disorder.

Background: The rat intestinal fatty acid-binding protein (I-FABP) is expressed in the small intestine and is involved in the absorption and transport of dietary fatty acids. It is used as a marker for intestinal injury and is associated with various gastrointestinal disorders. I-FABP has been studied extensively using conventional experimental and computational techniques.

Insights into the structural properties of SARS-CoV-2 main protease.

SARS-CoV-2 is the infectious agent responsible for the coronavirus disease since 2019, which is the viral pneumonia pandemic worldwide. The structural knowledge on SARS-CoV-2 is rather limited. These limitations are also applicable to one of the most attractive drug targets of SARS-CoV-2 proteins - namely, main protease M, also known as 3C-like protease (3CL).

Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins.

Computer simulations are used for identifying the secondary structure properties of ordered and disordered proteins. However, our recent studies showed that the chosen computer simulation protocol, simulation technique, and force field parameter set for a disordered protein impact its predicted secondary structure properties. Here, we compare the outcome from computer simulations utilizing molecular dynamics simulations without parallel tempering techniques using various force field parameter sets and temperature-replica exchange molecular dynamics simulations both for a model ordered and two model disordered proteins.

Structures of MERS-CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and CHARMM36m and AMBER99SB force field parameters.

A novel virus, severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) worldwide appeared in 2019. Detailed scientific knowledge of the members of the Coronaviridae family, including the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is currently lacking. Structural studies of the MERS-CoV proteins in the current literature are extremely limited.