Molecular dynamics of ferrocytochrome c: Time dependence of the atomic displacements

Structural, kinetic and thermodynamic characterizations of SDS-induced molten globule state of a highly negatively charged cytochrome c

This study presents the structural, kinetic and thermodynamic characterizations of previously unknown submicellar concentrations of SDS-induced molten globule (MGSDS) state of a highly negatively charged base-denatured ferricytochrome c (UB-state) at pH ∼12.8 (±0.2). The far-UV CD, near-UV CD, ANS-fluorescence data of UB-state in the presence of different concentrations of SDS indicate that the submicellar concentrations of SDS (≤0.4 mM) transform the UB-state to MGSDS-state. The MGSDS-state has native-like α-helical secondary structure but lacks tertiary structure. The free energy change (ΔG°D) for UB→ MGSDS transition determined by far-UV CD (∼2.7 kcal mol-1) is slightly higher than those determined by fluorescence (∼2.0 kcal mol-1) at 25°C. At very low SDS and NaCl concentrations, the MGSDS-state undergoes cold denaturation. As SDS concentration is increased, the thermal denaturation temperature increases and the cold denaturation temperature decrease. Kinetic experiments involving the measurement of the CO-association rate to the base-denatured ferrocytochrome c at pH ≈12.8 (±0.2), 25°C indicate that the submicellar concentrations of SDS restrict the internal dynamics of base-denatured protein.

Protein stiffening and entropic stabilization in the subdenaturing limit of guanidine hydrochloride

Subdenaturing concentrations of guanidine hydrochloride (GdnHCl) stabilize proteins. For ferrocytochrome c the stabilization is detected at subglobal level with no measured change in global stability. These deductions are made by comparing observed rates of thermally driven ferrocytochrome cHCO reactions with global unfolding rates of ferrocytochrome c measured by stopped flow and NMR hydrogen exchange in the presence of a wide range of GdnHCl concentrations at pH 7, 22 degrees C.

Molecular dynamics of sickle and normal hemoglobins

Molecular dynamics (MD) simulations have been carried out for 62.5 ps on crystal structures of deoxy sickle cell hemoglobin (HbS) and normal deoxy hemoglobin (HbA) using the CHARMM MD algorithm, with a time step of 0.001 ps. In the trajectory analysis of the 12.5-62.5 (50 ps) simulation, oscillations of the radius of gyration and solvent-accessible surface area were calculated. HbS exhibited a general contraction during the simulation, while HbA exhibited a nearly constant size. The average deviations of simulated structures from the starting structures were found to be 1.8 A for HbA and 2.3 A for HbS. The average rms amplitudes of atomic motions (atomic flexibility) were about 0.7 A HbA and about 1.0 A for HbS. The amplitudes of backbone motion correlate well with temperature factors derived from x-ray crystallography. A comparison of flexibility between the alpha- and beta-chains in both HbA and HbS indicates that the beta-chains generally exhibited greater flexibility than the alpha-chains, and that the HbS beta-chains exhibit greater flexibility in the N-terminal and D- and F-helix regions than do those of HbA. The average amplitude of backbone torsional oscillations was about 9 degrees, a value comparable with that of other simulations, with enhanced torsional oscillation occurring primarily at the ends of helices or in loop regions between helices. Comparison of atomic flexibility and torsional oscillation results suggests that the increased beta-chain flexibility results from relatively concerted motions of secondary structure elements. The increased flexibility may play an important role in HbS polymerization.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations

Molecular dynamics simulations of hen egg-white lysozyme in the free and substrate-bound states are reported and the nature of the average structures and atomic fluctuations are analyzed. Crystallographic water molecules of structural importance, as determined by hydrogen-bonding, were included in the simulations. Comparisons are made between the dynamics and the X-ray results for the atomic positions, the main-chain and side-chain dihedral angles, and the hydrogen-bonding geometry. Improvements over earlier simulations in the potential energy function and methodology resulted in stable trajectories with the C alpha co-ordinates within 1.5 A of the starting X-ray structure. Structural features analyzed in the simulations agreed well with the X-ray results except for some surface residues. The Asx chi 2 dihedral distribution and the geometry of hydrogen bonding at reverse turns show differences; possible causes are discussed. The relation between the magnitudes and time-scales of the residue fluctuations and secondary structural features, such as helices beta-sheets and coiled loops, is examined. Significant differences in the residue mobilities between the simulations of the free and substrate-bound states were found in a region of the enzyme that is in direct contact with the substrate and in a region that is distant from the active-site cleft. The dynamic behavior of the structural water molecules is analyzed by examining the correlation between the fluctuations of the water oxygens and the lysozyme heavy-atoms to which they are hydrogen-bonded.

Study of protein dynamics by X-ray diffraction

Properly carried out, high-resolution X-ray diffraction data collection followed by careful least-squares refinement can give the spatial distribution of the high-frequency mean-square displacements in a protein. These displacements reflect both individual atomic fluctuations in hard variables (bond lengths and bond angles) and collective motions involving soft variables (torsion angles, nonbonded interactions). Lower frequency, large amplitude motions and rapid but improbable motions are not quantifiable, but they may lead to such complete disorder that their existence can at least be inferred from the absence of interpretable electron density for some sections of the structure. Interior residues are more rigid than groups on the surface, and structural constraints are reflected in restricted motion even for surface residues. Amplitudes of motion of 0.5 A or greater are not uncommon. The temperature dependence of these fast motions varies considerably over the structure. In general, large [chi 2] values have large temperature dependence, while small displacements are less affected by temperature; however, exceptions are common. Significant reduction in [chi 2] on cooling establishes that proteins are mobile even in the crystalline state, and that static disorder is not the dominant contributor to the individual mean square displacements. Disordered regions in electron density maps are no longer automatically taken as signs of errors in structure determination. It is now recognized that the absence of strong electron density is often an indicator of conformational flexibility. Some of the functional roles for protein dynamics are beginning to be understood. Missing from these results are the physicochemical details that can be extracted from thermal motion analysis of small molecule crystal structures. Application of these methods to protein data is very difficult, but it is well to remember that just over 10 years ago it was commonly felt that protein structures could not even be refined. Certainly some small, well-diffracting proteins should be amenable to many of the sophisticated small-molecule analyses, as they yield X-ray data to resolutions comparable to simple organic structures. The most important type of analysis that awaits is anisotropic B factor refinement, which would give the principal directions of motion added to the amplitude information now obtained. Unfortunately, refinement of unrestrained anisotropic thermal elipsoids requires six parameters for each atom instead of a single isotropic B parameter, and even 1.5 A resolution data do not provide enough overdeterminacy.(ABSTRACT TRUNCATED AT 400 WORDS)