Heterogeneous Dynamical Environment at the Interface of a Protein-DNA Complex

Conformational Properties of Poly(A)-Binding Protein Complexed with Poly(A) RNA

Microscopic understanding of protein-RNA interactions is important for different biological activities, such as RNA transport, translation, splicing, silencing, etc. Polyadenine (Poly(A)) binding proteins (PABPs) make up a class of regulatory proteins that play critical roles in protecting the poly(A) tails of cellular mRNAs from nuclease degradation. In this work, we performed molecular dynamics simulations to investigate the conformational modifications of human PABP protein and poly(A) RNA that occur during complexation. It is demonstrated that the intermediate linker domain of the protein transforms from a disordered coil-like structure to a helical form during the recognition process, leading to the formation of the complex. On the other hand, disordered collapsed coil-like RNA on complexation has been found to transform into a rigid extended conformation. Importantly, the binding free energy calculation showed that the thermodynamic stability of the complex is primarily guided by favorable hydrophobic interactions between the protein and the RNA.

Roles of interfacial water states on advanced biomedical material design

When biomedical materials come into contact with body fluids, the first reaction that occurs on the material surface is hydration; proteins are then adsorbed and denatured on the hydrated material surface. The amount and degree of denaturation of adsorbed proteins affect subsequent cell behavior, including cell adhesion, migration, proliferation, and differentiation. Biomolecules are important for understanding the interactions and biological reactions of biomedical materials to elucidate the role of hydration in biomedical materials and their interaction partners. Analysis of the water states of hydrated materials is complicated and remains controversial; however, knowledge about interfacial water is useful for the design and development of advanced biomaterials. Herein, we summarize recent findings on the hydration of synthetic polymers, supramolecular materials, inorganic materials, proteins, and lipid membranes. Furthermore, we present recent advances in our understanding of the classification of interfacial water and advanced polymer biomaterials, based on the intermediate water concept.

Theoretical investigations on the effects of mutations in important residues of NS1B on its RNA-binding using molecular dynamics simulations

NS1B protein plays an important role in countering host antiviral defense and virulence of influenza virus B, considered as the promising target. The first experimental structure of the NS1B protein has recently been determined, was able to bind to double-stranded RNA (dsRNA). However, few studies attempt to investigate the RNA-binding mechanism of the NS1B. In this study, we provide our understanding of the structure-function relationship, dynamics and RNA-binding mechanism of the NS1B protein by performing molecular dynamics simulations combined and MM-GBSA calculations on the NS1B-dsRNA complex. 12 key residues are identified for RNA-binding by forming hydrogen bonds with the. Our results also demonstrate that mutations (R156A, K160A, R208A and K221A) can cause the local structure changes of NS1B CTD and the hydrogen bonds between NS1B CTD and RNA disappearance, which may be the main reasons for the decrease in RNA-binding affinity. These results mentioned will help us understanding the RNA-binding mechanism and could provide some medicinal chemistry insights chances for rational drug design targeting NS1B protein.