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. However, the detection of intrinsically disordered regions requires the application of special sampling molecular dynamics simulations along with certain bioinformatics because conventional computational and experimental studies face challenges in identifying the features of intrinsic disorder. METHOD: Replica exchange molecular dynamics simulations were conducted along with bioinformatics studies to gain deeper insights into the structural properties of I-FABP. Specifically, the Cα and Hα chemical shift values werecalculated, and the findings were compared to the experiments. Furthermore, secondary and tertiary structure properties were also calculated, and the protein was clustered using k-means clustering. The end-to-end distance and radius of gyration values were reported for the protein in an aqueous solution medium. In addition, its disorder tendency was studied using various bioinformatics tools. RESULTS AND CONCLUSION: It was reported that I-FABP is a flexible protein with regions that demonstrate intrinsic disorder characteristics. This flexibility and intrinsic disorder characteristics of I-- FABP may be related to its nature in ligand binding processes.

Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective.

Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycoproteins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.