Hydrogen-exchange evidence for distinct structural classes in globular proteins

A dynamic hydrophobic core orchestrates allostery in protein kinases

Eukaryotic protein kinases (EPKs) constitute a class of allosteric switches that mediate a myriad of signaling events. It has been postulated that EPKs' active and inactive states depend on the structural architecture of their hydrophobic cores, organized around two highly conserved spines: C-spine and R-spine. How the spines orchestrate the transition of the enzyme between catalytically uncommitted and committed states remains elusive. Using relaxation dispersion nuclear magnetic resonance spectroscopy, we found that the hydrophobic core of the catalytic subunit of protein kinase A, a prototypical and ubiquitous EPK, moves synchronously to poise the C subunit for catalysis in response to binding adenosine 5'-triphosphate. In addition to completing the C-spine, the adenine ring fuses the β structures of the N-lobe and the C-lobe. Additional residues that bridge the two spines (I150 and V104) are revealed as part of the correlated hydrophobic network; their importance was validated by mutagenesis, which led to inactivation. Because the hydrophobic architecture of the catalytic core is conserved throughout the EPK superfamily, the present study suggests a universal mechanism for dynamically driven allosteric activation of kinases mediated by coordinated signal transmission through ordered motifs in their hydrophobic cores.

Proteolytically-induced changes of secondary structural protein conformation of bovine serum albumin monitored by Fourier transform infrared (FT-IR) and UV-circular dichroism spectroscopy

Enzymatically-induced degradation of bovine serum albumin (BSA) by serine proteases (trypsin and α-chymotrypsin) in various concentrations was monitored by means of Fourier transform infrared (FT-IR) and ultraviolet circular dichroism (UV-CD) spectroscopy. In this study, the applicability of both spectroscopies to monitor the proteolysis process in real time has been proven, by tracking the spectral changes together with secondary structure analysis of BSA as proteolysis proceeds. On the basis of the FTIR spectra and the changes in the amide I band region, we suggest the progression of proteolysis process via conversion of α-helices (1654 cm(-1)) into unordered structures and an increase in the concentration of free carboxylates (absorption of 1593 and 1402 cm(-1)). For the first time, the correlation between the degree of hydrolysis and the concentration of carboxylic groups measured by FTIR spectroscopy was revealed as well. The far UV-CD spectra together with their secondary structure analysis suggest that the α-helical content decreases concomitant with an increase in the unordered structure. Both spectroscopic techniques also demonstrate that there are similar but less spectral changes of BSA for the trypsin attack than for α-chymotrypsin although the substrate/enzyme ratio is taken the same.

Infrared spectroscopic studies on reaction induced conformational changes in the NADH ubiquinone oxidoreductase (complex I)

Redox-dependent conformational changes are currently discussed to be a crucial part of the reaction mechanism of the respiratory complex I. Specialized difference Fourier transform infrared techniques allow the detection of side-chain movements and minute secondary structure changes. For complex I, (1)H/(2)H exchange kinetics of the amide modes revealed a better accessibility of the backbone in the presence of NADH and quinone. Interestingly, the presence of phospholipids, that is crucial for the catalytic activity of the isolated enzyme complex, changes the overall conformation. When comparing complex I samples from different species, very similar electrochemically induced FTIR difference spectra and very similar rearrangements are reported. Finally, the information obtained with variants and from Zn(2+) inhibited samples for the conformational reorganization of complex I upon electron transfer are discussed in this review. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.

Protein dynamics: from rattling in a cage to structural relaxation

We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.

Analysis of proton exchange kinetics with time-dependent exchange rate

Mass spectrometry is used to probe the kinetics of hydrogen-deuterium exchange in lysozyme in pH 5, 6 and 7.4. An analysis based on a Verhulst growth model is proposed and effectively applied to the kinetics of the hydrogen exchange. The data are described by a power-like function which is based on a time-dependence of the exchange rate. Experimental data ranging over many time scales is considered and accurate fits of a power-like function are obtained. Results of fittings show correlation between faster hydrogen-deuterium exchange and increase of pH. Furthermore a model is presented that discriminates between easily exchangeable hydrogens (located in close proximity to the protein surface) and those protected from the exchange (located in the protein interior). A possible interpretation of the model and its biological significance are discussed.

Membrane protein dynamics: limited lipid control

Correlation of lipid disorder with membrane protein dynamics has been studied with infrared spectroscopy, by combining data characterizing lipid phase, protein structure and, via hydrogen-deuterium (H/D) exchange, protein dynamics. The key element was a new measuring scheme, by which the combined effects of time and temperature on the H/D exchange could be separated. Cyanobacterial and plant thylakoid membranes, mammalian mitochondria membranes, and for comparison, lysozyme were investigated. In dissolved lysozyme, as a function of temperature, H/D exchange involved only reversible movements (the secondary structure did not change considerably); heat-denaturing was a separate event at much higher temperature. Around the low-temperature functioning limit of the biomembranes, lipids affected protein dynamics since changes in fatty acyl chain disorders and H/D exchange exhibited certain correlation. H/D exchange remained low in all membranes over physiological temperatures. Around the high-temperature functioning limit of the membranes, the exchange rates became higher. When temperature was further increased, H/D exchange rates went over a maximum and afterwards decreased (due to full H/D exchange and/or protein denaturing). Maximal H/D exchange rate temperatures correlated neither with the disorder nor with the unsaturation of lipids. In membrane proteins, in contrast to lysozyme, the onsets of sizable H/D exchange rates were the onsets of irreversible denaturing as well. Seemingly, at temperatures where protein self-dynamics allows large-scale H/D exchange, lipid-protein coupling is so weak that proteins prefer aggregating to limit the exposure of their hydrophobic surface regions to water. In all membranes studied, dynamics seemed to be governed by lipids around the low-temperature limit, and by proteins around the high-temperature limit of membrane functionality.PACS codes: 87.14.ep, 87.14.cc, 87.16.D.

Structure and molecular mobility of soy glycinin in the solid state

We report a multitechnique study of structural organization and molecular mobility for soy glycinin at a low moisture content (<30% w/w) and relate these to its glass-to-rubber transition. Small-angle X-ray scattering (SAXS), differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy are used to probe structure and mobility on different length and time scales. NMR (approximately 10(-6) to 10(-3) s) reveals transitions at a higher moisture content (>17%) than DSC or SAXS, which sample for much longer times (approximately 10 to 10(3) s) and where changes are detected at >13% water content at 20 degrees C. The mobility transitions are accompanied by small changes in unit-cell parameters and IR band intensities and are associated with the enhanced motion of the polypeptide backbone. This study shows how characteristic features of the ordered regions of the protein (probed by SAXS and FTIR) and mobile segments (probed by NMR and DSC) can be separately monitored and integrated within a mobility transformation framework.

Infrared spectroscopy study on the conformational changes leading to pore formation of the toxin sticholysin II

The structure of the actinoporin sticholysin II (StnII) in the pore state was investigated by Fourier transform infrared spectroscopy in the attenuated total reflection configuration. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/cholesterol unilamellar vesicles were employed. The alpha-helix content increases in approximately 30% upon lipid binding, which agrees with an extension of eight or nine residues at the N-terminal helix. Furthermore, analyses of dichroic spectra show that the extended N-terminal helix would have a 31 degrees tilt with respect to the membrane normal. The orientation of the central beta-sandwich was also estimated. In addition, it was detected that StnII alters the orientation of the lipid acyl chains. (1)H/(2)H exchange experiments sustain a mainly superficial interaction between StnII and the membrane, with no protection of the beta-sandwich. The implications of the results in the mechanism of pore formation are discussed.

Influence of hydration on the dynamics of lysozyme

Quasielastic neutron and light-scattering techniques along with molecular dynamics simulations were employed to study the influence of hydration on the internal dynamics of lysozyme. We identified three major relaxation processes that contribute to the observed dynamics in the picosecond to nanosecond time range: 1), fluctuations of methyl groups; 2), fast picosecond relaxation; and 3), a slow relaxation process. A low-temperature onset of anharmonicity at T approximately 100 K is ascribed to methyl-group dynamics that is not sensitive to hydration level. The increase of hydration level seems to first increase the fast relaxation process and then activate the slow relaxation process at h approximately 0.2. The quasielastic scattering intensity associated with the slow process increases sharply with an increase of hydration to above h approximately 0.2. Activation of the slow process is responsible for the dynamical transition at T approximately 200 K. The dependence of the slow process on hydration correlates with the hydration dependence of the enzymatic activity of lysozyme, whereas the dependence of the fast process seems to correlate with the hydration dependence of hydrogen exchange of lysozyme.

Controlling the protein dynamical transition with sugar-based bioprotectant matrices: a neutron scattering study

Through elastic neutron scattering we measured the mean-square displacements of the hydrogen atoms of lysozyme embedded in a glucose-water glassy matrix as a function of the temperature and at various water contents. The elastic intensity of all the samples has been interpreted in terms of the double-well model in the whole temperature range. The dry sample shows an onset of anharmonicity at approximately 100 K, which can be attributed to the activation of methyl group reorientations. Such a protein intrinsic dynamics is decoupled from the external environment on the whole investigated temperature range. In the hydrated samples an additional and larger anharmonic contribution is provided by the protein dynamical transition, which appears at a higher temperature Td. As hydration increases the coupling between the protein internal dynamics and the surrounding matrix relaxations becomes more effective. The behavior of Td that, as a function of the water content, diminishes by approximately 60 K, supports the picture of the protein dynamics as driven by solvent relaxations. A possible connection between the protein dynamical response versus T and the thermal stability in glucose-water bioprotectant matrices is proposed.

Conditioning action of the environment on the protein dynamics studied through elastic neutron scattering

The dynamics of lysozyme in the picosecond timescale has been studied when it is in dry and hydrated powder form and when it is embedded in glycerol, glycerol-water, glucose and glucose-water matrices. The investigation has been undertaken through elastic neutron scattering technique on the backscattering spectrometer IN13. The dynamics of dry powder and embedded-in-glucose lysozyme can be considered purely vibrational up to 100 K, where the onset of an anharmonic contribution takes place. This contribution can be attributed to the activation of methyl group reorientations and is described with an Arrhenius trend. An additional source of anharmonic dynamics appears at higher temperatures for lysozyme in hydrated powders and embedded in glycerol, glycerol-water and glucose-water matrices. This second process, also represented with an Arrhenius trend, corresponds to the so-called protein dynamical transition. Both the temperature where such a transition takes place and the magnitude of the protein mean square displacements depend on the environment. The dynamical response of the protein to temperature is put in relationship with its thermal stability.

Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration

The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.

Picosecond internal dynamics of lysozyme as affected by thermal unfolding in nonaqueous environment

A neutron-scattering investigation of the internal picosecond dynamics of lysozyme solvated in glycerol as a function of temperature in the range 200-410 K has been undertaken. The inelastic contribution to the measured intensity is characterized by the presence of a bump generally known as "boson peak", clearly distinguishable at low temperature. When the temperature is increased the quasielastic component of the spectrum becomes more and more intrusive and progressively overwhelms the vibrational bump. This happens especially for T > 345 K when the protein goes through an unfolding process, which leads to the complete denaturation. The quasielastic term is the superposition of two components whose intensities and linewidths have been studied as a function of temperature. The slower component describes motions with characteristic times of approximately 4 ps corresponding to reorientations of polypeptide side chains. Both the intensity and linewidth of this kind of relaxations show two distinct regimes with a crossover in the temperature range where the melting process occurs, thus suggesting the presence of a dynamical transition correlated to the protein unfolding. Conversely the faster component might be ascribed to the local dynamics of hydrogen atoms caged by the nearest neighbors with characteristic time of approximately 0.3 ps.

Hydrogen-deuterium exchange in membrane proteins monitored by IR spectroscopy: a new tool to resolve protein structure and dynamics

As more and more high-resolution structures of proteins become available, the new challenge is the understanding of these small conformational changes that are responsible for protein activity. Specialized difference Fourier transform infrared (FTIR) techniques allow the recording of side-chain modifications or minute secondary structure changes. Yet, large domain movements remain usually unnoticed. FTIR spectroscopy provides a unique opportunity to record (1)H/(2)H exchange kinetics at the level of the amide proton. This approach is extremely sensitive to tertiary structure changes and yields quantitative data on domain/domain interactions. An experimental setup designed for attenuated total reflection and a specific approach for the analysis of the results is described. The study of one membrane protein, the gastric H(+),K(+)-ATPase, demonstrates the usefulness of (1)H/(2)H exchange kinetics for the understanding of the molecular movement related to the catalytic activity.

Uses of enthalpy-entropy compensation in protein research

Cooperative systems of proteins and small molecules form most of biology but are so weakly linked that conventional mass-law formalism requiring exact stoichiometry is inapplicable. The weaknesses cannot be eliminated but using selected families of reactions useful fragmentation of those quantities is often possible. Extra-thermodynamic treatments based on linear-free-energy relationships (LFE) are developed to utilize enthalpy, entropy and volume information not otherwise reliable Linkage systems build around mesophilic proteins are well suited to enforced marriage of linear equations and scaled molecule detail because the ratio of substructure sizes on which folded stability depends is independent of total number of amino-acid residues. Conformational changes in physiological function usually no greater than 0.5 A closely scale to linear thermodynamic changes. The formalisms for use of LFE and compensation relationships are modified to eliminate complications that have previously arisen from incorrect inclusion of the thermal parts of enthalpy and entropy changes in free energy changes. The results are used to remove current confusion about the basis of folded stability in proteins and to minimize the quantitative errors arising from classical treatments of denaturation data. The enthalpy to entropy ratio given by the slope of a compensation plot (its 'compensation temperature') is used to characterize protein construction and function so as to extract machine descriptions of protein linkage systems. In this way the 'fragile' nature of the free-energy surfaces of the myoglobin proteins and the 'strong' character of those surfaces of most other mesophiles can be deduced very simply from the Debye-Waller factors obtained in diffraction studies. The major evolutionary achievement in making proteins big is their crystallike phase behavior. That makes entropy exactly as important as enthalpy so the scalar quantities of small-molecule chemistry can be replaced by the vector quantities that appear necessary to make biology possible.

Structural effects of drying and rehydration for enzymes in soils: a kinetics-FTIR analysis of α-chymotrypsin adsorbed on montmorillonite

The effects of desiccation and rehydration cycles encountered by extracellular enzymes in soils are studied on -chymotrypsin adsorbed on montmorillonite. The controlled hygrometric FTIR cell used in this study enables to monitor drying and rehydration steps undergone by the -chymotrypsin-montmorillonite suspension or by the enzyme alone. Relative humidity (RH) determines the amount of deuterated water in the FTIR cell atmosphere. The molar water/protein ratio (W/P) as well as the conformational and solvation states of the enzyme have been determined using H/D exchange monitored by FTIR-transmission spectroscopy. When the W/P ratio decreases from 3500 to approximately 400, unfolding of beta-secondary structure in three different domains involves about 8% of the polypeptide backbone with respect to the most solvated states. Desiccation induces beta-unfolding, which opens channels allowing free vapor water molecules to diffuse into the enzyme at 15% RH. On drying to 0% RH, displacements of internal water (H2O) in the enzyme are demonstrated by reverse peptide isotopic exchanges (COND ==> CONH). Specific beta-structures, only formed in highly solvated states, sequester around 20 internal H2O molecules. Indeed, most of the unfolded secondary structures during the drying step are refolded at W/P approximately 1000 during rehydration. However, self-association hinders the recovery of the initial closed tertiary structure. The pD-dependent structural changes controlling inward and outward water diffusion are suppressed, whether the protein is initially in an adsorbed state or in solution. Changes in secondary structures encountered during desiccation/rehydration cycle are similar for the protein either free or in the adsorbed state. Thus domains that are unfolded by adsorption are not concerned by the desiccation/rehydration cycle.

Analysis of 1H/2H exchange kinetics using model infrared spectra

This paper investigates the different approaches that best retrieve band shape parameters and kinetic time constants from series of protein Fourier transform infrared (FT-IR) spectra recorded in the course of 1H/2H exchange. In this first approach, synthetic spectra were used. It is shown that 1H/2H exchange kinetic measurements can help resolve spectral features otherwise hidden because of the overlap of various spectral contributions. We evaluated the efficiency of Fourier self-deconvolution, synchronous/asynchronous correlation, difference spectroscopy, principal component analysis, inverse Laplace transform, and determination of the underlying spectra by global analysis assuming first-order kinetics with either known or unknown time constants. It is demonstrated that some strategies allow the extraction of both the time dependence and the spectral shape of the underlying contributions.

Attenuated total reflection IR spectroscopy as a tool to investigate the orientation and tertiary structure changes in fusion proteins

Membrane fusion proceeds via a merging of two lipid bilayers and a redistribution of aqueous contents and bilayer components. It involves transition states in which the phospholipids are not arranged in bilayers and in which the monolayers are highly curved. Such transition states are energetically unfavourable since biological membranes are submitted to strong repulsive hydration electrostatic and steric barriers. Viral membrane proteins can help to overcome these barriers. Viral proteins involved in membrane fusion are membrane associated and the presence of lipids restricts drastically the potential of methods (RMN, X-ray crystallography) that have been used successfully to determine the tertiary structure of soluble proteins. We describe here how IR spectroscopy allows to solve some of the problems related to the lipid environment. The principles of the method, the experimental setup and the preparation of the samples are briefly described. A few examples illustrate how attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy can be used to gain information on the orientation and the accessibility to the water phase of the fusogenic domain of viral proteins. Recent developments suggest that the method could also be used to detect changes located in the membrane domains and to identify intermediate structural states involved in the fusion process.

Detection of structural and functional asymmetries in P-glycoprotein by combining mutagenesis and H/D exchange measurements

During the last few years, Attenuated Total Reflection Fourier Transform Infrared spectroscopy (ATR-FTIR) has become one of the most powerful methods to determine the structure of biological materials and in particular of components of biological membranes, like proteins which cannot be studied by X-ray crystallography and NMR. Indeed, ATR-FTIR method requires little amount of material, gives valuable information about the secondary structure, orientation and tertiary structure changes in peptides and proteins. Moreover, this technique can be used in the presence of lipids and hence provides an excellent tool to study membrane proteins in their natural environment. In this review, we describe how structural information about the catalytic cycle of membrane proteins can be gained by combining ATR-FTIR spectroscopy and mutagenesis. In particular, results obtained about the structure and function of the nucleotide binding domains (NBD) of P-glycoprotein (Pgp), a multidrug transporter involved in cancer cells resistance to chemotherapy, are described.

Protein substructures and folded stability

Protein substructures detected in proton-exchange experiments can be described in quantitative detail with the Debye-Waller temperature factors from diffraction studies. The smallest substructures, in mesophilic proteins approximately 12% of the total residues, determine thermodynamic as well as kinetic stability by electrostatic synergism of a few tightly packed clusters about central peptide-peptide hydrogen bonds. Fixed positions of the clusters establish genetic stability of a protein family. The normal product of thermal denaturation above 280 K in dilute buffers, a compact but motile bubble, is formed with positive free-energy change in step from native state the single transition state and smaller negative change in the step from transition state to product. The largest substructures, approximately 80% of the residues, undergo changes in atom free volumes in function that are small relative to coordinate errors in protein diffraction studies but nevertheless describe the most important conformation changes. The criterion of precision in protein construction is approximately 0.05 A and may be found to be smaller when precision in X-ray diffraction improves. The ratio of residues in the two substructures is fixed in mesophiles.

Parsimony in protein evolution

Pohl found the activation enthalpy and entropy for melting of his mesophilic proteins to be linear in the total number of residues and Privalov and colleagues found this same linearity for the standard heat-capacity, enthalpy and entropy changes in the overall melting equilibria. Despite the small samples these results suggest that mesophiles individually, and as a class, are related through a single standard representative. If so, very extensive convergent evolution has provided both great simplification and very sophisticated goals for genome decoding and quantitative description of protein substructures [R. Lumry, The protein primer, http://www.umn.edu.chem. /groupslumry].

Conformational changes and orientation of Humicola lanuginosa lipase on a solid hydrophobic surface: an in situ interface Fourier transform infrared-attenuated total reflection study

This study was done to better understand how lipases are activated at an interface. We investigated the conformational and solvation changes occurring during the adsorption of Humicola lanuginosa lipase (HLL) onto a hydrophobic surface using Fourier transform infrared-attenuated total reflection spectroscopy. The hydrophobic surfaces were obtained by coating silicon attenuated total reflection crystal with octadecyltrichlorosilane. Analysis of vibrational spectra was used to compare the conformation of HLL adsorbed at the aqueous-solid interface with its conformation in solution. X-ray crystallography has shown that HLL exists in two conformations, the closed and open forms. The conformational changes in HLL caused by adsorption onto the surface were compared with those occurring in three reference proteins, bovine serum albumin, lysozyme, and alpha-chymotrypsin. Adsorbed protein layers were prepared using proteins solutions of 0.005 to 0.5 mg/mL. The adsorptions of bovine serum albumin, lysozyme, and alpha-chymotrypsin to the hydrophobic support were accompanied by large unfoldings of ordered structures. In contrast, HLL underwent no secondary structure changes at first stage of adsorption, but there was a slight folding of beta-structures as the lipase monolayer became complete. Solvation studies using deuterated buffer showed an unusual hydrogen/deuterium exchange of the peptide CONH groups of the adsorbed HLL molecules. This exchange is consistent with the lipase being in the native open conformation at the water/hydrophobic interface.

Study of amide-proton exchange of Escherichia coli melibiose permease by attenuated total reflection-Fourier transform infrared spectroscopy: evidence of structure modulation by substrate binding

The accessibility of Escherichia coli melibiose permease to aqueous solvent was studied following hydrogen-deuterium exchange kinetics monitored by attenuated total reflection-Fourier transform infrared spectroscopy under four distinct conditions where MelB forms different complexes with its substrates (H(+), Na(+), melibiose). Analysis of the amide II band upon (2)H(2)O exposure discloses a significant sugar protection of the protein against aqueous solvent, resulting in an 8% less exchange of the corresponding H(+)*melibiose*MelB complex compared with the protein in the absence of sugar. Investigation of the amide I exchange reveals clear substrate effects on beta-sheet accessibility, with the complex H(+)*melibiose*MelB being the most protected state against exchange, followed by Na(+)*melibiose*MelB. Although of smaller magnitude, similar changes in alpha-helices plus non-ordered structures are detected. Finally, no differences are observed when analyzing reverse turn structures. The results suggest that sugar binding induces a remarkable compactness of the carrier's structure, affecting mainly beta-sheet domains of the transporter, which, according to secondary structure predictions, may include cytoplasmic loops 4-5 and 10-11. A possible catalytic role of these two loops in the functioning of MelB is hypothesized.

Attenuated total reflection IR spectroscopy as a tool to investigate the structure, orientation and tertiary structure changes in peptides and membrane proteins

During the last few years, attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) has become one of the most powerful methods to determine the structure of biological materials and in particular of components of biological membranes, like proteins that cannot be studied by x-ray crystallography and NMR. ATR-FTIR requires a little amount of material (1-100 microg) and spectra are recorded in a matter of minutes. The environment of the molecules can be modulated so that their conformation can be studied as a function of temperature, pressure, pH, as well as in the presence of specific ligands. For instance, replacement of amide hydrogen by deuterium is extremely sensitive to environmental changes and the kinetics of exchange can be used to detect tertiary conformational changes in the protein structure. Moreover, in addition to the conformational parameters that can be deduced from the shape of the infrared spectra, the orientation of various parts of the molecule can be estimated with polarized IR. This allows more precise analysis of the general architecture of the membrane molecules within the biological membranes. The present review focuses on ATR-IR as an experimental approach of special interest for the study of the structure, orientation, and tertiary structure changes in peptides and membrane proteins.

Resolved fluorescence of the two tryptophan residues in horse apomyoglobin

The composite fluorescence emission from the two tryptophans (W7 and W14) of horse heart apomyoglobin was explored by fluorescence quenching experiments. The fluorescence of the W7 residue is the only one involved in the quenching by iodide or trichloroethanol (TCE) titration. The fluorescence contribution of W7 is 49% of the total apomyoglobin emission, and its spectrum is red-shifted compared to the W14 emission. The fluorescence decay of Trp residues gives an average fluorescence lifetime of 2.06 ns for W14 and 2.84 ns for W7. The static fluorescence quenching by TCE was used to monitor the individual motions of the two tryptophans in apomyoglobin. The short correlation time of W7 (rho = 3 ns) explains why this residue can experience various environments without having to assume the existence of several protein conformations occurring during its lifetime emission.

Hydrogen/deuterium exchange kinetics of apolipophorin-III in lipid-free and phospholipid-bound states. An analysis by Fourier transform infrared spectroscopy

Attenuated total reflection Fourier transform infrared spectroscopy was used to probe the kinetics of hydrogen/deuterium exchange in Manduca sexta apolipophorin-III (apoLp-III). ApoLp-III is an exchangeable apolipoprotein that is made up of five elongated amphipathic alpha-helices in a helical bundle conformation in the monomeric lipid-free form. Upon interaction with phospholipids, it is postulated to undergo a large conformational change whereby the hydrophobic interior is exposed, facilitating binding to the lipid surfaces. We have used the lipid-free and dimyristoylphosphatidylcholine-bound apoLp-III to study the dynamically variable domains in the two forms. Three populations of amide protons varying in their hydrogen/deuterium exchange rates were found to exist: slow, intermediate, and fast exchanging, which could correspond to completely buried, partially buried, and solvent-exposed domains on the protein in both the states. In lipid-free apoLp-III, 36, 12, and 52% of the total residues contributed to the slow, intermediate, and fast exchanging populations, respectively. In the dimyristoylphosphatidylcholine-bound form, the corresponding distribution was 20, 16, and 64%, representing a 12% increase in the number of exposed residues. The results are discussed in terms of increased solvent accessibility due to gross tertiary structural reorganization.

Access of ligands to cavities within the core of a protein is rapid

We have investigated the magnitude and timescale of fluctuations within the core of a protein using the exchange kinetics of indole and benzene binding to engineered hydrophobic cavities in T4 lysozyme. The crystal structures of variant-benzene complexes suggest that relatively large scale fluctuations (1-2 angstrom) of backbone atoms are required for entry of these ligands into the core. Nonetheless, these ligands enter the cavities rapidly, with bimolecular rate constants of approximately 10(6)-10(7) M(-1) s(-1) and a low activation barrier, 2-5 kcal mol(-1). These results suggest that protein cores undergo substantial fluctuations on the millisecond to microsecond timescale and that entry of small molecules into protein interiors is not strongly limited by steric occlusion.

Time-resolved room temperature protein phosphorescence: nonexponential decay from single emitting tryptophans

The single room temperature phosphorescent (RTP) residue of horse liver alcohol dehydrogenase (LADH). Trp-314, and of alkaline phosphatase (AP), Trp-109, show nonexponential phosphorescence decays when the data are collected to a high degree of precision. Using the maximum entropy method (MEM) for the analysis of these decays, it is shown that AP phosphorescence decay is dominated by a single Gaussian distribution, whereas for LADH the data reveal two amplitude packets. The lifetime-normalized width of the MEM distribution for both proteins is larger than that obtained for model monoexponential chromophores (e.g., terbium in water and pyrene in cyclohexane). Experiments show that the nonexponential decay is fundamental; i.e., an intrinsic property of the pure protein. Because phosphorescence reports on the state of the emitting chromophore, such nonexponential behavior could be caused by the presence of excited state reactions. However, it is also well known that the phosphorescence lifetime of a tryptophan residue is strongly dependent on the local flexibility around the indole moiety. Hence, the nonexponential phosphorescence decay may also be caused by the presence of at least two states of different local rigidity (in the vicinity of the phosphorescing tryptophan) corresponding to different ground state conformers. The observation that in the chemically homogeneous LADH sample the phosphorescence decay kinetics depends on the excitation wavelength further supports this latter interpretation. This dependence is caused by the wavelength-selective excitation of Trp-314 in a subensemble of LADH molecules with differing hydrophobic and rigid environments. With this interpretation, the data show that interconversion of these states occurs on a time scale long compared with the phosphorescence decay (0.1-1.0 s). Further experiments reveal that with increasing temperature the distributed phosphorescence decay rates for both AP and LADH broaden, thus indicating that either 1) the number of conformational states populated at higher temperature increases or 2) the temperature differentially affects individual conformer states. The nature of the observed heterogeneous triplet state kinetics and their relationship to aspects of protein dynamics are discussed.

Reverse micelles as a water-property-control system to investigate the hydration/activity relationship of alpha-chymotrypsin

alpha-Chymotrypsin, solubilized in hydrated reverse micelles of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) in n-octane, was used as a model system for studying the involvement of different water structures (strongly bound water, disordered water, water clusters and bulk water) in the development of the catalytically active conformation of the enzyme. Results presented in this study indicate a characteristic dependence of the stability/activity profile on the water content of the reverse-micellar system for values of wo of approximately 5 (wo is defined as [H2O]/[AOT]). The results are consistent with heat-capacity measurements for proteins. At very low wo values, the conformation of alpha-chymotrypsin changes to a very rigid structure in comparison to the structure observed in water. This is demonstrated by the overall center of gravity of the tryptophan fluorescence spectrum of the enzyme at wo = 0.65, which is blue shifted in comparison to the spectrum in bulk water indicating that the enzyme is in an apolar environment. In the absence of a hydration shell, the protein is to a great extent frozen and inactive. A small increase in the level of enzyme hydration (up to wo = 2.3) causes an increase in the amount of strongly bound water associated with the enzyme and the enzyme displays a high catalytic activity. Upon further addition of water, a new unstable water structure with unfavourable enthalpy is developed and the enzyme activity declines, reaching a minimum at wo = 5.1. A new increase of water content within a relatively small range, wo = 5-8, causes a dramatic increase in enzymic activity, reminiscent of a cooperative hydration dependence. In the range wo = 10-29, the effect of hydration on the activity is complete which shows that the enzyme activity depends on the amount of water in contact with the enzyme and not on the total amount of bulk water in the system. The experimental results on enzyme incubation at different wo values followed by dilution to constant high wo, are indicative of inactive conformational substates of alpha-chymotrypsin. It is demonstrated that highly active enzyme conformations at very low, wo values occur via an induced fit mechanism of substrate binding.

The influence of hydration on the conformation of bovine serum albumin studied by solid-state 13C-NMR spectroscopy

13C proton-decoupled cross-polarization magic-angle spinning nmr spectra of bovine serum albumin are reported as a function of hydration. Increases in hydration level enhance the resolution of the peak centered at about 40 ppm but has little or no effect on the other spectral peaks. Hydration has little effect on either the rotating frame proton spin-lattice relaxation time or the cross-relaxation time for any of the peaks, suggesting that the efficiency of dipolar coupling is largely preserved on hydration of the protein. Resolution enhancement of the peak at 40 ppm is not understood, but possible sources of the behavior include a decrease in the line width of contributing resonances from lysine epsilon carbons due to increased motional averaging on hydration, reordering of disulfide bridges, and titration shifts induced by hydration. Hydration of bovine serum albumin appears to have little effect on the distribution of conformations sampled by the protein so that the broad distribution of conformations observed in the dry state is also observed in the fully hydrated state. This is in contrast to lysozyme where significant ordering of the conformation is seen on hydration.

Hydrogen exchange identifies native-state motional domains important in protein folding

Effects of mutations on hydrogen exchange kinetics, structure, and stability suggest that the slow exchange core is a key element in protein folding. Single amino acid variants of bovine pancreatic trypsin inhibitor (BPTI) have been made with glycine or alanine replacement of residues Tyr 35, Gly 37, Asn 43, and Asn 44. The crystal structures of Y35G and N43G are reported [Housset, D., Kim, K.-S., Fuchs, J., & Woodward, C. (1991) J. Mol. Biol. 220, 757-770; Danishefsky, A. T., Housset, D., Kim, K.-S., Tao, F., Fuchs, J., Woodward, C., & Wlodawer, A. (1993) Protein Sci. 2, 577-587; Kim, K.-S., Tao, F., Fuchs, J. A., Danishefsky, A. T., Housset, D., Wlodawer, A., & Woodward, C. (1993a) Protein Sci. 2, 588-596]. NMR chemical shifts indicate few changes from the wild type (WT) in G37A and N44G. Stabilities of the four mutants were measured by calorimetry and by hydrogen exchange. Values of delta delta(WT-->mut), the difference in delta G of folding/unfolding between the wild type and mutant, estimated by both methods are in good agreement and are in the range 4.7-6.0 kcal/mol. There is no general correlation between stability and hydrogen exchange rates at pH 3.5 and 30 degrees C. Exchange occurs by two parallel pathways, one involving small noncooperative fluctuations of the native state, and the other involving cooperative, global unfolding. In the mutant proteins, the rates for exchange by the unfolding mechanism are accelerated by a factor corresponding to the increase in the unfolding/folding equilibrium constant.(ABSTRACT TRUNCATED AT 250 WORDS)

The influence of hydration on the conformation of lysozyme studied by solid-state 13C-NMR spectroscopy

13C proton decoupled cross-polarization magic-angle spinning nmr spectra of lysozyme are reported as a function of hydration. Increases in hydration level enhance the resolution of the spectra, particularly in the aliphatic region, but has no significant effect on either the rotating frame proton spin-lattice relaxation time or the cross-relaxation time. The enhancement in spectral resolution with hydration is attributed to a decrease in the distribution of isotropic chemical shifts, which reflects a decrease in the distribution of conformational states sampled by the protein. Changes in the distribution of isotropic chemical shifts occur after the addition of water to the charged groups as coverage of the polar side chains and peptide groups takes place. The onset of this behavior occurs at a hydration level of about 0.1-0.2 g water/g protein and is largely complete at about 0.3 g water/g protein, the same hydration range where changes in the heat capacity are observed. That hydrogen exchange of buried protons can occur at hydration levels significantly lower than those at which changes in the distribution of conformational states are first observed suggests that some motions that mediate exchange are already present in the dry protein. The preservation of efficient dipolar coupling indicates that the conformational rearrangements that do occur on hydration are small and do not involve any significant overall expansion of free volume or weakening of interactions that would increase the reorientational freedom of protein groups.

Characterization of the backbone dynamics of an anti-digoxin antibody VL domain by inverse detected 1H-15N NMR: comparisons with X-ray data for the Fab

The dynamic behavior of the polypeptide backbone of a recombinant antidigoxin antibody VL domain has been characterized by measurements of 15NT1 and T2 relaxation times, 1H-15N NOE values, and 1H-2H exchange rates. These data were acquired with 2D inverse detected heteronuclear 1H-15N NMR methods. The relaxation data are interpreted in terms of model free spectral density functions and exchange contributions to transverse relaxation rates R2 (= 1/T2). All characterized residues display low-amplitude picosecond time-scale librational motions. Fifteen residues undergo conformational changes on the nanosecond timescale, and 24 residues have significant R2 exchange contributions, which reflect motions on the microsecond to millisecond time-scale. For several residues, microsecond to millisecond motions of nearby aromatic rings are postulated to account for some or all of their observed R2 exchange contributions. The measured 1H-2H exchange rates are correlated with hydrogen bonding patterns and distances from the solvent accessible surface. The degree of local flexibility indicated by the NMR measurements is compared to crystallographic B-factors derived from X-ray analyses of the native Fab and the Fab/digoxin complex. In general, both the NMR and X-ray data indicate enhanced flexibility in the turns, hypervariable loops, and portions of beta-strands A, B, and G. However, on a residue-specific level, correlations among the various NMR data, and between the NMR and X-ray data, are often absent. This is attributed to the different dynamic processes and environments that influence the various observables. The combined data indicate that certain regions of the VL domain, including the three hypervariable loops, undergo dynamic changes upon VL:VH association and/or complexation with digoxin. Overall, the 26-10 VL domain exhibits relatively low flexibility on the ps-ns timescale. The possible functional consequences of this result are considered.

Tryptophan phosphorescence of G-actin and F-actin

The tryptophan phosphorescence spectrum, intensity and decay kinetics of G-actin and F-actin were measured over a temperature range of 140-293 K. The fine structure in the phosphorescence spectra at low temperature, with O,O vibrational bands centered at 405 nm and 415.5 nm for both species, reveals a marked heterogeneity of the chromophore environment. The thermal quenching profile distinguishes these sites in terms of their flexibility, and shows that probably only one of the four tryptophan residues is still phosphorescent at ambient temperature due to its location in a relatively rigid buried core. Although some differences are demonstrated between G-actin and F-actin at low temperature, the identity of the triplet lifetime at ambient temperature strongly supports the notion that the conformation of the macromolecule is largely unaffected by polymerization. Preliminary phosphorescence anisotropy measurements demonstrate both the occurrence of singlet-singlet energy transfer among tryptophan residues and a strong immobilization of actin in the polymerized state.