Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques

Abstract

Almost all proteins fold via a number of partially structured intermediates such as molten globule (MG) and pre-molten globule states. Understanding the structure of these intermediates at atomic level is often a challenge, as these states are observed under extreme conditions of pH, temperature, and chemical denaturants. Furthermore, several other processes such as chemical modification, site-directed mutagenesis (or point mutation), and cleavage of covalent bond of natural proteins often lead to MG like partially unfolded conformation. However, the dynamic nature of proteins in these states makes them unsuitable for most structure determination at atomic level. Intermediate states studied so far have been characterized mostly by circular dichroism, fluorescence, viscosity, dynamic light scattering measurements, dye binding, infrared techniques, molecular dynamics simulations, etc. There is a limited amount of structural data available on these intermediate states by nuclear magnetic resonance (NMR) and hence there is a need to characterize these states at the molecular level. In this review, we present characterization of equilibrium intermediates by biophysical techniques with special reference to NMR.

Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications

“…Molecular dynamic (MD) simulations of chitinase provided a detailed information on the fluctuations and conformational changes . MD simulations can track system behavior and understanding of protein folding (Ubaid-Ullah et al 2014;Haque et al 2015;Naiyer et al 2015). These methods are used to investigate the structure, dynamics and thermodynamics of biological molecules (Anwer et al 2015;Hoda et al 2015;Naz et al 2015).…”

Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E

“…1B) monitored by  222 as a function of [urea], that at nearly 4.0-4.4 M concentration of urea, a stable conformation is achieved, which is more stable than native one (we named this state as X state), while at 6.0M HFE gets completely denatured (D state) ( Table 2) [46]. We found that secondary structure retained in X state, lies in the range 40-50% of that of N state, this implies that X state possess one of the structural characteristics of PMG state (the retention of near about 50% secondary structure of the native protein) [5,58].…”

Nucleotide-free kinesin motor domains reversibly convert to an inactive conformation with characteristics of a molten globule

“…ANS has low fluorescence in water and in the presence of compact folded proteins that do not allow the dye access to their hydrophobic interior, but becomes highly fluorescent when bound to molten globules that largely retain secondary structure but have a loose ternary conformation that allow access of the dye to the hydrophobic interior[24,25]. Conversion of a molten globule to a fully unfolded protein, however, reduces the fluorescence of ANS, likely because hydrophobic clusters are no longer present.…”