Utsab Shrestha

Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile

Significance Deep-sea microorganisms can adapt to extreme conditions of high temperature and pressure. What makes these organisms survive and reproduce in such critical conditions remains an open question. Here, we use the quasielastic neutron scattering (QENS) technique to study the dynamic behavior of a hyperthermophilic protein that is found in the deep sea. Our results give evidence that high pressure affects the dynamical properties of proteins by distorting the protein energy landscape in ways that are significantly different for hyperthermophilic and mesophilic proteins. Consequently, a general schematic denaturation phase diagram together with energy landscapes for the two different proteins are derived, and this approach can be used as a general picture to understand the effects of pressure on protein dynamics and activities. Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric protein derived from a hyperthermophilic microorganism that is found near hydrothermal vents deep under the sea, where the pressure is up to 100 MPa (1 kbar). It has attracted great interest in biophysical research because of its high activity under extreme conditions in the seabed. In this study, we use the quasielastic neutron scattering (QENS) technique to investigate the effects of pressure on the conformational flexibility and relaxation dynamics of IPPase over a wide temperature range. The β-relaxation dynamics of proteins was studied in the time ranges from 2 to 25 ps, and from 100 ps to 2 ns, using two spectrometers. Our results indicate that, under a pressure of 100 MPa, close to that of the native environment deep under the sea, IPPase displays much faster relaxation dynamics than a mesophilic model protein, hen egg white lysozyme (HEWL), at all measured temperatures, opposite to what we observed previously under ambient pressure. This contradictory observation provides evidence that the protein energy landscape is distorted by high pressure, which is significantly different for hyperthermophilic (IPPase) and mesophilic (HEWL) proteins. We further derive from our observations a schematic denaturation phase diagram together with energy landscapes for the two very different proteins, which can be used as a general picture to understand the dynamical properties of thermophilic proteins under pressure.

Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor

Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to significant structural fluctuations of the protein embedded within the membrane yielding the activation of cognate G-protein (transducin), which initiates biological signaling. Here, we report a quasi-elastic neutron scattering study of the activation of rhodopsin as a GPCR prototype. Our results reveal a broadly distributed relaxation of hydrogen atom dynamics of rhodopsin on a picosecond-nanosecond time scale, crucial for protein function, as only observed for globular proteins previously. Interestingly, the results suggest significant differences in the intrinsic protein dynamics of the dark-state rhodopsin versus the ligand-free apoprotein, opsin. These differences can be attributed to the influence of the covalently bound retinal ligand. Furthermore, an idea of the generic free-energy landscape is used to explain the GPCR dynamics of ligand-binding and ligand-free protein conformations, which can be further applied to other GPCR systems.

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

In this article, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA), and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak noncovalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA. Our results clearly suggest that the protein conformational flexibility and rigidity are balanced by the native protein structure for biological activity.

Influence of molecular shape on self-diffusion under severe confinement: A molecular dynamics study

Abstract We have investigated the effect of molecular shape and charge asymmetry on the translation dynamics of confined hydrocarbon molecules having different shapes but similar kinetic diameters, inside ZSM-5 pores using molecular dynamics simulations. The mean square displacement of propane, acetonitrile, acetaldehyde, and acetone in ZSM-5 exhibit two different regimes – ballistic and diffusive/sub-diffusive. All the molecules except propane exhibit sub-diffusive motion at time scales greater than 1 ps. The intermediate scattering functions reveal that there is a considerable rotational-translational coupling in the motion of all the molecules, due to the strong geometrical restriction imposed by ZSM-5. Overall the difference in shape and asymmetry in charge imposes severe restriction inside the ZSM-5 channels for all the molecules to different extents. Further, the behavior of molecules confined in ZSM-5 in the present study, quantified wherever possible, is compared to their behavior in bulk or in other porous media reported in literature.