Graduate Group in Biochemistry and Molecular Biophysics and the Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia 19104, United States.
Published: October 2013
AI Article Synopsis
Article Abstract
Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven proteins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion--the NMR-derived generalized order parameters--as a proxy from which to derive changes in protein conformational entropy.
Group of Characterization of Materials, Departament de Física, Universitat Politècnica de Catalunya, Campus Diagonal-Besòs, Av. Eduard Maristany 10-14, Barcelona 08019, Spain.
Hybrid organic-inorganic perovskites (HOIP) have emerged in recent years as highly promising semiconducting materials for a wide range of optoelectronic and energy applications. Nevertheless, the rotational dynamics of the organic components and many-molecule interdependencies, which may strongly impact the functional properties of HOIP, are not yet fully understood. In this study, we quantitatively analyze the orientational disorder and molecular correlations in archetypal perovskite CHNHPbI (MAPI) by performing comprehensive molecular dynamics simulations and entropy calculations.
In this study, the interaction mechanism between Si quantum dots (SiQDs) and bovine serum albumin (BSA), as well as the conformational and functional alterations of BSA, were rigorously investigated via multispectral techniques and dynamic light scattering analysis. van der Waals forces and hydrogen bonding, as well as an exothermic reaction and a decrease in entropy, were the primary forces involved in the binding of SiQDs to BSA. In the binding process, SiQDs exhibit preferential proximity to Site I over other potential binding sites.
We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP)-the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based theory explicitly considers the size, shape, conformation, charge, and chemical state of all molecular species-thereby linking the structural state with the chemical/charged state of the system. We investigate how variations in monovalent and divalent salt concentrations, as well as pH, affect the charge distribution across different regions of an NCP and quantify the impact of charge regulation.
The mis-folding and aggregation of intrinsically disordered proteins (IDPs) such as α-synuclein (αS) underlie the pathogenesis of various neurodegenerative disorders. However, targeting αS with small molecules faces challenges due to the lack of defined ligand-binding pockets in its disordered structure. Here, we implement a deep artificial neural network-based machine learning approach, which is able to statistically distinguish the fuzzy ensemble of conformational substates of αS in neat water from those in aqueous fasudil (small molecule of interest) solution.
The dengue virus (DENV) NS5 protein plays a central role in dengue viral RNA synthesis which makes it an attractive target for antiviral drug development. DENV NS5 is known to interact with the stem-loop A (SLA) promoter at the 5'-untranslated region (5'-UTR) of the viral genome as a molecular recognition signature for the initiation of negative strand synthesis at the 3' end of the viral genome. However, the conformational dynamics involved in these interactions are yet to be fully elucidated.
