Influence of pressure on structure and dynamics of bovine pancreatic trypsin inhibitor (BPTI): small angle and quasi-elastic neutron scattering studies

High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration

High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the CheY-FliM interface. PaCS-MD enabled us to observe pressure-induced dissociation of the CheY-FliM complex at atomic resolution. Pressure dependence of binding free energy indicates that the increase of pressure from 0.1 to 100 MPa significantly weakens the binding. Using high-pressure microscopy, we observed that high hydrostatic pressure fixes the motor rotation to the counter-clockwise direction. In conclusion, the application of pressure enhances hydration of the proteins and weakens the binding of CheY to FliM, preventing reversal of the flagellar motor.

Effects of Hydrodynamic Interactions on the Near-Surface Diffusion of Spheroidal Molecules

We investigated diffusion of spheroidal molecules near a planar surface, accounting for spatially dependent translational and rotational mobilities of molecules resulting from their hydrodynamic interactions with the plane. Rigid-body Brownian dynamics simulations of prolate ellipsoids of revolution of an axial ratio in the range of 1.5 to 3.0, suspended in a viscous fluid, with a no-slip flat boundary confining the suspension were employed. Mobility tensor matrices of molecules were evaluated as functions of spheroids' distance and orientation with respect to the plane. Hydrodynamic interactions with the surface lead to substantial changes of spheroids' translational diffusion coefficients both in the direction perpendicular and parallel to the plane when compared with the values characterizing the bulk diffusion. Moreover, the short-time translational diffusion of molecules, measured in the laboratory frame, both in an unbounded fluid and under the confinement, is non-Gaussian, with much larger deviations from Gaussianity observed in the latter case. In an unbounded fluid, distributions of translational displacements of molecules deviate from those expected for a simple Brownian motion as a result of shape anisotropy. In the presence of the plane, spheroids experience an additional anisotropic drag, and consequently, their mobilities depend on their positions and orientations. Therefore, anomalies in the short-time dynamics observed under confinement can be explained in terms of the so-called diffusing-diffusivity mechanism. Our findings have implications for understanding of a wide range of biological and technological processes that involve diffusion of anisotropic molecules near surfaces of natural and model cell membranes, biosensors and nanosensors, and electrodes.

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

BACKGROUND

Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations.

SCOPE OF REVIEW

First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure.

MAJOR CONCLUSIONS

Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening.

GENERAL SIGNIFICANCE

MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.

A high pressure cell using metallic windows to investigate the structure of molecular solutions up to 600 MPa by small-angle neutron scattering

We report on a high pressure (HP) cell designed for the determination of the structure of molecular solutions by small-angle neutron scattering (SANS). The HP cell is fitted up with two thick metallic windows that make the device very resistant under hydrostatic pressures up to 600 MPa (or 6 kbar). The metallic windows are removable, offering the possibility to adapt the HP cell to a given study with the pressure desired on an appropriate spatial range to study the structure of various molecular solutions by SANS. In this context, we report the absorption, transmission, and scattering properties of different metallic windows. Finally, we describe, as a proof of principle, the solution structure changes of myoglobin, a small globular protein.

Pressure effects on collective density fluctuations in water and protein solutions

Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces.

High hydrostatic pressure: a probing tool and a necessary parameter in biophysical chemistry

High pressures extending up to several thousands of atmospheres provide extreme conditions for biological organisms to survive. Recent studies are investigating the survival mechanisms and biological function of microorganisms under natural and laboratory conditions extending into the GigaPascal range, with applications to understanding the Earth's deep biosphere and food technology. High pressure has also emerged as a useful tool and physical parameter for probing changes in the structure and functional properties of biologically important macromolecules and polymers encountered in soft matter science. Here we highlight some areas of current interest in high pressure biophysics and physical chemistry that are emerging at the frontier of this cross-disciplinary field.

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

The Anton supercomputing technology recently developed for efficient molecular dynamics simulations permits us to examine micro- to milli-second events at full atomic resolution for proteins in explicit water and lipid bilayer. It also permits us to investigate to what extent the collective motions predicted by network models (that have found broad use in molecular biophysics) agree with those exhibited by full-atomic long simulations. The present study focuses on Anton trajectories generated for two systems: the bovine pancreatic trypsin inhibitor, and an archaeal aspartate transporter, GltPh. The former, a thoroughly studied system, helps benchmark the method of comparative analysis, and the latter provides new insights into the mechanism of function of glutamate transporters. The principal modes of motion derived from both simulations closely overlap with those predicted for each system by the anisotropic network model (ANM). Notably, the ANM modes define the collective mechanisms, or the pathways on conformational energy landscape, that underlie the passage between the crystal structure and substates visited in simulations. In particular, the lowest frequency ANM modes facilitate the conversion between the most probable substates, lending support to the view that easy access to functional substates is a robust determinant of evolutionarily selected native contact topology.

Atomic-scale dynamics inside living cells explored by neutron scattering

Single-particle neutron spectroscopy has contributed important experimental data on molecular dynamics in biological systems. The technique provides information on atomic and molecular motions in macromolecules on the picosecond to the nanosecond time scale, which are essential to biological function. Here, we report on recent neutron measurements performed directly in living cells by using isotope labelling to explore the dynamics of specific cellular components. The paper proposes an integrated view of results on atomic-scale cell water dynamics, internal and global macromolecular motions and solvent isotope effect on macromolecular dynamics. The work established the specific usefulness of the neutron scattering technique to get insight into biologically relevant dynamical features, in particular through comparative measurements. The method developed can now be applied to look for dynamical signatures related to cell characteristics in many different cell types and organelles.

Self-similar dynamics of proteins under hydrostatic pressure-Computer simulations and experiments

Different experimental techniques, such as kinetic studies of ligand binding and fluorescence correlation spectroscopy, have revealed that the diffusive, internal dynamics of proteins exhibits autosimilarity on the time scale from microseconds to hours. Computer simulations have demonstrated that this type of dynamics is already established on the much shorter nanosecond time scale, which is also covered by quasielastic neutron scattering experiments. The autosimilarity of protein dynamics is reflected in long-time memory effects in the underlying diffusion processes, which lead to a non-exponential decay of the observed time correlation functions. Fractional Brownian dynamics is an empirical model which is able to capture the essential aspects of internal protein dynamics. Here we give a brief introduction into the theory and show how the model can be used to interpret neutron scattering experiments and molecular dynamics simulation of proteins in solution under hydrostatic pressure.

Temperature dependence on structure and dynamics of Bovine Pancreatic Trypsin Inhibitor (BPTI): a neutron scattering study

We have studied the influence of temperature on the structure of BPTI in solution by small angle neutron scattering. We have investigated the variation of the radius of gyration and the modification of the shape of BPTI between ambient temperature and 368 K. Results have shown an increase of the radius of gyration from 10.9 A at ambient temperature up to 13.3 A at 368 K. Global and internal dynamics of BPTI in solution were studied by quasielastic neutron scattering. The analysis of neutron data in terms of intermediate scattering function reveals two relaxation times tau(1) and tau(2) related respectively to global translational diffusive motions and to internal motions of protein. Motions of protons belonging to lateral chains of residues located at the surface of the protein have been detected. The results are compared to the recently published results concerning the influence of pressure on structure and dynamics of BPTI in solution [Appavou MS et al. Biochimica et Biophysica Acta, 1764, 2006, pp 414-423].

New sources and instrumentation for neutrons in biology

Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.

In vivo measurement of internal and global macromolecular motions in Escherichia coli

We present direct quasielastic neutron scattering measurements, in vivo, of macromolecular dynamics in Escherichia coli. The experiments were performed on a wide range of timescales to cover the large panel of internal and self-diffusion motions. Three major internal processes were extracted at physiological temperature: a fast picosecond process that corresponded to restricted jump diffusion motions and two slower processes that resulted from reorientational motions occurring in approximately 40 ps and 90 ps, respectively. The analysis of the fast process revealed that the cellular environment leads to an appreciable increase in internal molecular flexibility and diffusive motion rates compared with those evaluated in fully hydrated powders. The result showed that the amount of cell water plays a decisive role in internal molecular dynamics. Macromolecular interactions and confinement, however, attenuate slightly the lubricating effect of water, as revealed by the decrease of the in vivo parameters compared with those measured in solution. The study demonstrated that standard sample preparations do not mimic accurately the physiological environment and suggested that intracellular complexity participates in functional dynamics necessary for biological activity. Furthermore, the method allowed the extraction of the self-diffusion of E. coli macromolecules, which presented similar parameters as those extracted for hemoglobin in red blood cells.

Structural evolution during protein denaturation as induced by different methods

Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been used to study conformational changes in protein bovine serum albumin (BSA) due to perturbation in its native structure as induced by varying temperature and pressure, and in presence of protein denaturating agents urea and surfactant. BSA has prolate ellipsoidal shape at ambient temperature and we observe no effect of temperature on its structure up to a temperature of about 60 degrees C . At temperatures beyond 60 degrees C , protein denaturation leads to aggregation. The protein solution exhibits a fractal structure at temperatures above 64 degrees C , and its fractal dimension increases with temperature. This is an indication of aggregation followed by gelation that evolves with increasing temperature. It is known for some of the proteins (e.g., Staphylococcal Nuclease) that pressure of 200 MPa can unfold the protein, whereas BSA does not show any protein unfolding even up to the pressure of 450 MPa . In presence of urea, the BSA protein unfolds for urea concentrations greater than 4M and acquires a random coil configuration. We make use of the dilution method to show the reversibility of protein unfolding with urea. The addition of surfactant denaturates the protein by the formation of micellelike aggregates of surfactants along the unfolded polypeptide chains of the protein. We show such structure of the protein-surfactant complex can be stabilized at higher temperatures, which is not the case for pure protein.