Traditional macromolecular crystallography (MX) and recently spotlighted cryogenic electron microscopy (Cryo-EM) techniques have contributed greatly to the development of macromolecule structures related fields [...]

Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments - in this article, we feature aqueous systems involving polymers, surfactants and proteins - the link between dyn...

Mean macromolecular dynamics was quantified in vivo by neutron scattering in psychrophile, mesophile, thermophile and hyperthermophile bacteria. Root mean square atomic fluctuation amplitudes determining macromolecular flexibility were found to be similar for each organism at its physiological temperature ( approximately 1 A in the 0.1 ns timescale). Effective force constants determining the me...

In the present study an attempt was made to investigate the macromolecular crowding effect on functional attributes of α-amylase. High concentrations of sugar based cosolvents, (e.g., trehalose, sucrose, sorbitol, and glycerol) were used to mimic the macromolecular crowding environment (of cellular milieu) under in vitro conditions. To assess the effect of macromolecular crowding, the activity ...

Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the effect on thermal requires estimate combined effects excluded volume, specific protein-environment interactions, as well response crowders. Here, we explore an ideal model system, lysozyme powder state, to dissect factors controlling melting under extreme crowding. By deploying state-of-the a...

Antioxidants are vital for aerobic life, and for decades the expectations of antioxidants as health promoting agents were very high. However, relatively recent meta-analyses of clinical studies show that supplementation of antioxidants does not result in the presumed health benefit, but is associated with increased mortality. The dilemma that still needs to be solved is: what are antioxidants i...

In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy...

Self-organization in macromolecular systems refers to the transition from a random assembly of interacting oligomers to a system of stable heteropolymers. The concept of adaptive value describes the correlation between environmental variability and the variability in replication and mutation rates of the interacting oligomers. This paper describes a model of self-organization in macromolecular ...

-We have designed an improved method for solving the embedding problem, which consists in generating molecular conformations satisfying prescribed distance restraints. The problem was broken up into smaller subproblems by carrying out separate embeddings of subsets of the original point set. The relative orientation of the subsets were then determined by an additional embedding and the final co...

at Spelman College, worked with Pankaj Agarwal and Yusu Wang, who just completed her PhD, at Duke. Hillary’s summer project was about analyzing the performance of the algorithm developed at Duke to generate features on a molecular surface. The features are then used to predict good configurations for protein docking. For efficiency reasons, we would like to use as few features as possible. The ...