Temperature-dependent X-ray diffraction as a probe of protein structural dynamics

An X-ray study of the physiological-temperature form of hen egg-white lysozyme at 2 A resolution

The structure of the high-temperature orthorhombic form of hen egg-white lysozyme has been determined at 2.0 A resolution. Initial images of the molecule were obtained at 6.0 A resolution both by double isomorphous replacement and by molecular replacement with use of the known structure of the room-temperature tetragonal lysozyme. The initial model thus obtained (R = 0.52 at 6.0 A) was refined first as a rigid body at 6.0 A and then by restrained least squares at 2.5 A and later at 2.0 A resolution. The final model (R = 0.23 at 2.0 A) was compared with that of the tetragonal form: the structures are very similar with a root mean square difference in superimposed alpha-carbon coordinates of 0.46 A. There are, however, differences which are caused by a crystal contact involving the upper part of this active site in the high-temperature orthorhombic form. Because of this, residues Trp 62 and Pro 70 are much better ordered than in the tetragonal form, where they are exposed to solvent. These differences can partly explain the difficulty of inhibitor-binding in high-temperature orthorhombic crystals, but do not seem to reflect the particular behaviour of lysozyme in solution at high temperature.

[Dynamics of protein structures]

This review presents a survey of experimental and theoretical methods capable of providing a many-parameter characterization of internal mobility of protein molecules. Special emphasis is on applications of high-resolution nuclear magnetic resonance for studies of non-crystalline proteins and discussions of possible correlations between protein dynamics and biological functions of proteins.

Conformational flexibility of membrane proteins in electric fields

Bacteriorhodopsin of halobacterial purple membranes exhibits conformational flexibility in high electric field pulses (1-30 x 10(5) V m(-1), 1-100 micros). High-field electric dichroism data of purple membrane suspensions indicate two kinetically different structural transitions within the protein; involving a rapid (approximately 1 micros) concerted change in the orientation of both retinal and tyrosine and/or tryptophan side chains concomitant with alterations in the local protein environment of these chromophores. as well as slower changes (approximately 100 micros) of the microenvironment of aromatic amino acid residues concomitant with pK changes in at least two types of proton-binding sites. Light scattering data are consistent with the maintenance of the random distribution of the membrane discs within the short duration of the applied electric fields. The kinetics of the electro-optic signals and the steep dependence of the relaxation amplitudes on the electric field strength suggest a saturable induced-dipole mechanism and a rather large reaction dipole moment of 1.1 x 10(-25) C m ( = 3.3 x 10(4) debye) per cooperative unit at E = 1.3 x 10(5) V m(-1), which is indicative of appreciable cooperativity in the probably unidirectional transversal displacement of ionic groups on the surfaces of and within the bacteriorhodopsin proteins of the membrane lattice. The electro-optic data of bacteriorhodopsin are suggestive of a possibly general, induced-dipole mechanism for electric field-dependent structural changes in membrane transport proteins such as the gating proteins in excitable membranes or the ATP synthetases.

Protein engineering

The prospects for protein engineering, including the roles of x-ray crystallography, chemical synthesis of DNA, and computer modelling of protein structure and folding, are discussed. It is now possible to attempt to modify many different properties of proteins by combining information on crystal structure and protein chemistry with artificial gene synthesis. Such techniques offer the potential for altering protein structure and function in ways not possible by any other method.

Dynamics of heme iron in crystals of metmyoglobin and deoxymyoglobin

The 57Fe gamma-ray resonance absorption spectra have been measured in crystals of metmyoglobin and deoxymyoglobin over a wide range of temperatures. Above a critical temperature common to both proteins (220 K), the dynamics of heme iron display a dramatic change, in that two kinds of thermal fluctuations come into play--a fast fluctuation associated with a steep decrease of the total fluctuation of characteristic time 10(-8) sec, associated with bounded diffusive motion. By using both discrete jump and continuous diffusion models, the latter based on the Brownian motion of an overdamped harmonic oscillator, the essential parameters of the iron motion (mean square displacement and jump frequency or diffusion constant) can be derived as a function of temperature. Thus, for deoxy Mb at 288 K, the mean square displacement for the fast fluctuation is about 6 X 10(-2) A2 and for the diffusive motion is 1.6 X 10(-2) A2; the diffusion constant is 4 X 10(-10) cm2/sec. The diffusive process is associated with an activation energy of about 0.75 kcal/mol. Although the same general kinds of phenomena are observed in crystals of MetMb and deoxy Mb, significant differences in behavior are found, which suggest that the main dynamical phenomenon observed reflects internal large-scale motions of the protein.

Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes

The experimental observations described in this article indicated that a distribution of many different fluctuations is present in a globular protein. These fluctuations were characterized by observation of many natural internal probes such as the labile peptide protons and the aromatic side chains. The conditions which are necessary to get reactions of the internal probes have been discussed in detail. The structural interpretation of the data was facilitated by the development and the use of new NMR techniques which provided the identification of the resonances of all the labile peptide protons. With NOE measurements a distinction between correlated and uncorrelated exchange events was obtained. This enabled us to elucidate the exchange mechanism over a wide range of p2H and temperature and to classify different subsets of fluctuations with respect to their lifetimes. It was further demonstrated that a change of external conditions such as temperature, p2H or pressure can change the distribution of fluctuations in the protein. The mechanisms responsible for rotation of internal aromatic side chains were also found to change with temperature, and mechanistic aspects of these fluctuations were discussed. This demonstration of a manifold of spatial fluctuations in a small protein provides an impression on the kind of fluctuations which have to be expected for larger proteins. When studying protein reactions one should therefore consider the presence of a large number of different, transiently formed, spatial structures available for the partner in the reaction, which may pick out only that structure which will optimally perform a particular reaction with the highest efficiency.

Adiabatic compressibility of globular proteins

The adiabatic compressibility of several globular proteins has been measured by using an ultrasonic technique in the frequency range 0.5 to 10 MHz. The contributions to the measured compressibility from the protein matrix and from surface processes involving ionization of side chains and solvation effects are discussed. The internal protein compressibility is very low, indicating the existence of "dynamic domains" which are tentatively assigned to secondary structure elements.

Unfolding processes of small globular proteins: the two-state vs multi-state model

1. The alcohol-induced unfolding of two homologous proteins, neurotoxin and cardiotoxin from Taiwan cobra (Naja naja atra) venom has been analysed. 2. It is postulated that the unfolding process for both proteins is a multi-state conformational transition. 3. It has been hypothesized that between the compact native state of the protein and its fully unfolded state there exists a quasi-continuous spectrum of conformational metastates of protein species. 4. The population distribution of these metastates is partially dependent on the nature of unfolding factors as well as the amino acid composition and sequence. 5. The sum of all transient conformational states and the protein species being in the folded and unfolded states respectively, can be detected by means of circular dichroism spectroscopy since the absorption of circularly polarized light is rapid relative to the rate of fluctuations of the protein structure.

Developments in low-temperature biochemistry and biology

Though under most circumstances harmful changes are induced in cellular structures by subzero temperatures, conditions can be found under which such damage is avoided. Thus, in solution, biochemical reactions can be slowed and more easily analysed and many enzyme-substrate complexes can be stabilized and structurally analysed; in crystals, 'stop-action' pictures unveil the stereochemical changes along reaction pathways. The progressive 'solidification' of non-covalent bonds involved in protein structures should permit investigation of their dynamics. Studies at high pressures open the way to new investigations on 'activated' enzyme-substrate complexes and might permit the refinement of current concepts to a considerable degree, as a preliminary but decisive step towards a full description of enzyme mechanisms. The conditions of medium allowing such cryobiochemical studies fail to protect cellular structures against cold. Investigations of plasma membrane behaviour are now under way to determine processes leading to cryosensitivity or cryotolerance of cells.

Electron paramagnetic resonance crystallography of bacterial catalase: g-Contour mapping method of analysis

Single crystals of bacterial catalase from Micrococcus luteus have been examined by EPR at 77 K. X-ray perfect crystals gave a set of four prominent resonances in all three orthogonal planes which yielded eight heme direction cosine matrices to an accuracy of +/- 2 degrees as expected for the P4(2)2(1)2 space group and unit cell parameters previously determined. These matrices are related by D4 symmetry operation of the space group. There were additional weaker resonances only resolved in two or even one plane. A method of g-contour mapping was devised to solve for the orientations of hemes that give rise to these weaker resonances. Three additional sets of heme orientations, also following D4 symmetry, were determined. All of the above sites have the same principal g values, 2.0, 5.4, and 6.6. The EPR crystallographic results imply that several conformational substates may be trapped at 77 K.

Hydrogen exchange and the dynamic structure of proteins

In native proteins, buried, labile protons undergo isotope exchange with solvent hydrogens, but the kinetics of exchange are markedly slower than in unfolded polypeptides. This indicates that, whereas buried protein atoms are shielded from solvent, the protein fluctuates around the time average structure and occasionally exposes buried sites to solvent. Generally, hydrogen exchange studies are designed to characterize the nature of the fluctuations between conformational substates, to monitor the shift in conformational equilibria among protein substates due to ligand binding or other factors, or to monitor the major cooperative denaturation transition. In this article, we review the recent reports of hydrogen exchange in proteins, focusing on recent advances in methodology, especially with regard to the implications of the results for the mechanism of hydrogen exchange in folded proteins.

Control and pH dependence of ligand binding to heme proteins

The recombination after flash photolysis of dioxygen and carbon monoxide with sperm whale myoglobin (Mb), and separated beta chains of human hemoglobin (beta A) and hemoglobin Zürich (beta ZH), has been studied as a function of pH and temperature from 300 to 60 K. At physiological temperatures, a preequilibrium is established between the ligand molecules in the solvent and in the heme pocket. The ligand in the pocket binds to the heme iron by overcoming a barrier at the heme. The association rate is controlled by this final binding step. The association rate of CO to Mb and beta A is modulated by a single titratable group with a pK at 300 K of 5.7. The binding of CO to beta ZH, in which the distal histidine is replaced by arginine, does not depend on pH. Oxygen recombination is independent of pH in all three proteins. Comparison of the binding of CO at 300 K and at low temperatures shows that pH does not affect the preequilibrium but changes the barrier height at the heme. The pH dependence and the difference between O2 and CO binding can be explained by a charge-dipole interaction between the distal histidine and CO.

Conformational substates in a protein: structure and dynamics of metmyoglobin at 80 K

The crystal structure of sperm whale metmyoglobin has been determined at 80 K to a resolution of 2A. The overall structure at 80 K is similar to that at 300 K except that the volume is smaller. Refinement of the structure by the method of restrained least squares (current R = 0.175) permits the assignment of isotropic atomic mean-square displacements to all nonhydrogen atoms. Comparison with the values obtained earlier at 250-300 K indicates that the protein at 80 K is more rigid. The average experimentally determined Debye-Waller factor, B, for the protein is 14A2 at 300 K and 5A2 at 80 K. Plots of backbone mean-square displacement vs. temperature show a discontinuity of slope for at least one-third of all residues. This behavior is in good agreement with the temperature dependence of the mean-square displacement of the heme iron as measured by Mössbauer absorption. The magnitudes of the smallest mean-square displacements observed at 80 K indicate that intramolecular motions can be frozen out to a surprisingly large degree. Even at 80 K, however, some atoms in myoglobin still have mean-square displacements greater than 0.1A2, thus providing evidence for conformational substates.

Structure of a B-DNA dodecamer at 16 K

The crystal structure of the B-DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G, previously solved and refined at room temperature (290 K), has been analyzed at 16 K (-257 degrees C). The end-to-end winding of the helix does not vary with temperature but remains constant at 10.1 base pairs per turn. Negatively charged phosphate groups throughout the structure do move closer together on cooling, however, probably because of increase in the dielectric constant of water as the temperature is lowered. This has the two-fold effect of reducing the spacing between neighboring double helices from 24.0 to 22.9 A and of narrowing the helix grooves within any isolated molecule. Overall lattice displacements as deduced from crystallographic temperature factors are very much decreased in the 16 K structure, yet displacements at phosphates continue to exceed those of deoxyribose sugars by B = 9 A2 and those of base pairs by B = 22 A2, even at this very low temperature at which practically all thermal motion has been eliminated. These differences, formerly interpreted as evidence for thermal vibration, must now be attributed to static disorder.

Infrared spectroscopy of photodissociated carboxymyoglobin at low temperatures

We have studied the infrared spectra of the bound and photodissociated states of Mb-12CO and Mb-13CO from 5.2 to 300 K. The absorbance peaks seen between 1800 and 2200 cm-1 correspond to CO stretching vibrations. In the bound state of Mb-12CO, the known lines A0 at 1969, A1 at 1945, and A2 at 1927 cm-1, have center frequencies, widths, and absorbances that are independent of temperature between 5.2 and 160 K. Above 160 K, A2 gradually shifts to 1933 cm-1. The low-temperature photodissociated state (Mb) shows three lines (B0, B1, B2) at 2144, 2131, and 2119 cm-1 for 12CO. The absorbances of the three lines depend on temperature. B0 is tentatively assigned to free CO in the heme pocket and B1 and B2, to CO weakly bound to the heme or heme pocket wall. The data are consistent with a model in which photodissociation of MbCO leads to B1 and B2. B2 decays thermally to B1 above 13 K; rebinding to A occurs from B1. The barriers between B2 and B1 and between B1 and A are described by activation enthalpy spectra. Heme and the central metal atom in state Mb have near-infrared, EPR, and Mössbauer spectra that differ slightly from those of deoxyMb. The observation of essentially free CO in state B implies that the difference between Mb and deoxyMb is not due to an interaction of the flashed-off ligand with the protein but is caused by an incomplete relaxation of the protein structure at low temperatures.

The pressure dependence of the spin equilibrium in camphor-bound ferric cytochrome P-450

The spin equilibrium of camphor-bound ferric cytochrome P-450 has been measured between 1-1000 bar (10(5)-10(8) Pa). Increasing pressure shifts the absorption spectrum from the high-spin form at 392 nm to the low-spin form at 417 nm. The molar volume change for the spin states delta V = -RT delta ln Ke/ delta P and the equilibrium coefficient Ke = [high spin]/[low spin] depend on the solvent conditions. At pH 5.6 the equilibrium coefficient at 1 bar, K1 = 0.5 and delta V = 312 cm3/mol. A sample with 10 mM KCl at pH 7 has K1 = 7.0 amd delta V = 52 cm3/mol. Solvent changes producing a larger K1 also result in a larger delta V which ranged over 16-74 cm3/mol. The correlation can be approximated as delta V = 36 + 18 log K1, which implies that there is a pressure, 3000 bar, for camphor-bound ferric cytochrome P-450 at 4 degrees C, at which the changes in delta V are compensated by the other thermodynamic parameters leaving Ke independent of the solvent conditions. Although the protein is not stable about 1000 bar for most sample conditions, the extrapolated log Ke versus pressure curves for all sample conditions intersect near 3000 bar. Camphor-bound cytochrome P-450 appears to be a rather flexible protein, having a low denaturing pressure, a large volume change, and a high sensitivity to the protein environment.

Protein dynamics investigated by the neutron diffraction-hydrogen exchange technique

A new approach, using neutron diffraction and the hydrogen exchange (H/D) technique, has been used to study the extent and nature of the inherent conformational fluctuations in the protein, trypsin. The observed pattern of exchange was used to investigate systematic relationships between exchangeable sites and structural and chemical properties of the molecule. Results of this analysis indicate that hydrogen-bonding structure is the dominant factor governing rates of exchange. The model of conformational mobility which best explains the experimental findings involves a localized disruption of the secondary structure within different regions of the protein molecule, each limited in extent to the breaking of a small number of hydrogen bonds.

Structural dynamics of erabutoxin b. A 13C nuclear magnetic resonance relaxation study of methyl groups

A detailed examination has been made of the 13C NMR relaxation times of the assigned methyl groups of erabutoxin b. Anisotropic rotation was analysed using a restricted diffusion model. The results are compared with a previous study of the 1H NMR relation times. There is good agreement on the segments of the molecule which show restricted motion. Our results are compared with those of previous studies on proteins in solution and in crystals and again the general agreement is good. We have attempted to interpret the value of the limited motion seen in the protein to the reactions of the neurotoxin.

Resonance Raman detection of structural dynamics at the active site in hemoglobin

The iron-histidine stretching mode in deoxyhemoglobin displays a large change in frequency and width upon lowering the temperature from 300 to 10 K. The temperature dependence of the data indicates the presence of dynamic process. The dynamics of this mode in frozen hemoglobins can be qualitatively and quantitatively described as a vibrational dephasing via anharmonic coupling to other vibrations of the heme-imidazole system. the effect that occur at the melting transition in the low frequency modes cannot be quantitatively addressed at this point but may be indicative of the introduction of additional degrees of freedom predicated on protein influences that reflect differences in protein quaternary structure.

Hydrogen exchange in RNase A: neutron diffraction study

Hydrogen exchange has been studied in a single crystal of RNase A [ribonuclease (pancreatic), EC 3.1.27.5] in the course of a neutron structure investigation. Refinement of the occupancies of amide hydrogens provided information about the kind of isotope present in each site and also provided estimates of the errors associated with the measurement. Twenty-eight of the 120 peptide amide hydrogens were found to be at least partially protected from exchange during approximately 1 year required for crystal preparation and data collection. Most of the protected hydrogens were involved in hydrogen bonds with main-chain carbonyl groups. A contiguous region of the beta-sheet containing residues 75, 106--109, 116, and 118 had a large number of protected hydrogens, indicating its low flexibility and the lack of accessibility to solvent. Residues 11--13 from the alpha-helix near the amino terminus were protected, in good agreement with a model of cooperative unwinding of this helix, starting from the free (amino) end.

Probing the energetics of proteins through structural perturbation: sites of regulatory energy in human hemoglobin

The sites of energy transduction within the human hemoglobin molecule for the regulation of oxygen affinity have been determined by an extensive study of the molecule's energetic response to structural alteration at individual amino acid residues. For 22 mutant and chemically modified hemoglobins we have determined the total free energy used by the tetrameric molecule for alteration of oxygen affinity at the four binding steps. The results imply that the regulation of oxygen binding affinity is due to energy changes which are mostly localized at the alpha 1 beta 2 interface. They also indicate a high degree of "internal cooperativity" within this contact region--i.e., the structural perturbations at individual residue sites are energetically coupled. Cooperativity in ligand binding is thus a reflection of cooperativity at a deeper level--that of the protein-protein interactions within the alpha 1 beta 2 interfacial domain.

Possible effects of 10(11) Hz radiation on the oxygen affinity of hemoglobin

When oxygen binds to one of the subunits of hemoglobin, the oxygen affinity of the other subunits is enhanced. This cooperative interaction of the subunits is initiated by the movement of the heme plane toward the proximal side when oxygen binds to the heme. This motion is transmitted to the surface of the globin through a "reaction channel" consisting of a group of atoms whose motion is well correlated. Considering the detailed geometry and X-ray diffraction data of the mean square displacement of the atoms surrounding the heme, a simple model for the heme plane oscillations is developed. Using this model, the natural frequency of oscillations is shown to be approximately 5 X 10(11) Hz. This result, along with the recent experimental data on the kinetics of the conformational changes of the heme, points to the possibility of radiation influencing the oxygen affinity of hemoglobin. If such an effect exists, it is likely that the oxygen affinity will be enhanced by the radiation.

Perspectives and outlook for electron microscopy in biology in general

The possibilities for improving methods of electron microscopy with the aim of visualizing still finer details of biological relevance are discussed with respect to different goals: discovering and defining new structures in situ, in the cell, in relation to functions, and investigating the fine structure of already morphologically and biochemically defined structures which are available in isolated and purified form. For each of these goals the importance of the inherent limitations are considered: lack of definition due to the unknown nature of heavy metal staining, deformations caused by the physical events of specimen preparation, and radiochemical alterations induced by the electron beam. Methods of investigating and overcoming these limitations by new cryotechniques, new imaging modes and improved crystallographic techniques are outlined. Emphasis is given to relevant biological phenomena, where electron microscopy is potentially the method of choice, e.g., those related to functional proteins situated in and on biological membranes and where relatively large conformational changes are supposed to have occurred to explain the functions.