The magnetic field and temperature dependences of proton spin-lattice relaxation in proteins

The nuclear magnetic relaxation dispersion profiles of lyophilized globular proteins were measured in the frequency range of 10 kHz-30 MHz at temperatures from 156 to 302 K. The existent theory of proton relaxation in immobilized protein systems was critically tested and expended to include contributions of rapid motions of protein side-chain groups. The new theory takes into account the strong coupling between the side-chain protons and the protein backbone, when correlation function cannot be written as a product of the contributions. The measurements showed that while the relaxation rate constant of the protein backbone protons is a linear function of the absolute temperature the side-chain groups exhibit an exponential temperature dependence corresponding to an activated process. Measurements carried out on simple homopolypeptides, polyglycine and polyalanine, provide strong support of the proposed new theory.     

Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping

Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.     

Multiple quantum filtered NMR studies of the interaction between collagen and water in the tendon

We studied the physical processes and the chemical reactions involved in magnetization transfer between water and large proteins, such as collagen, in bovine Achilles tendon. Since the NMR spectrum for such proteins is broadened by very large dipolar interactions, the NMR peaks of the various functional groups on the protein cannot be separated from one another on the basis of their different chemical shifts. A further complication in observing the protein spectrum is the intense narrow peak of the abundant water. Thus, magnetization transfer (MT) within the protein or between water and the protein cannot rely on differences in the chemical shifts, as is commonly possible in liquids. We present a method that separates the protein spectrum from that of the water spectrum on the basis of their different intramolecular dipolar interactions, enabling exclusive excitation of either the protein or water. As a result, the protein spectrum as well as the effect of spin diffusion within the protein can be measured. In addition, the MT rates from the protein to water and vice versa can be measured. Two types of mechanisms were considered for the MT: chemical exchange- and dipolar interaction-related processes (such as NOE). They were distinguished by examining the effects of the following experimental conditions: (a) temperature; (b) pH; (c) ratio of D(2)O to H(2)O in the bathing liquid; (d) interaction of the protein with small molecules other than water, such as DMSO and methanol. Our results lead us to the conclusion that the MT is dominated below the freezing point by the dipolar interaction between the protein and water, while an exchange of protons between the protein and the water molecules is the most significant process above the freezing point. On the basis of the fact that the spin temperature is established for the protein on a time scale much shorter than that of the MT, we could measure protein spectra that are distinguished by the contributions made to them by the various functional groups; i.e., contributions of methylenes were distinguished from those of methyls.     

An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange

A series of experiments are presented that provide an exchange-free measure of dipole-dipole (15)N transverse relaxation, R(dd), that can then be substituted for (15)N R(1rho) or R(2) rates in the study of internal protein dynamics. The method is predicated on the measurement of a series of relaxation rates involving (1)H-(15)N longitudinal order, anti-phase (1)H and (15)N single-quantum coherences, and (1)H-(15)N multiple quantum coherences; the relaxation rates of all coherences are measured under conditions of spin-locking. Results from detailed simulations and experiments on a number of protein systems establish that R(dd) values are independent of exchange and systematic errors from dipolar interactions with proximal protons are calculated to be less than 1-2%, on average, for applications to perdeuterated proteins. Simulations further indicate that the methodology is rather insensitive to the exact level of deuteration so long as proteins are reasonably highly deuterated (>50%). The utility of the methodology is demonstrated with applications involving protein L, ubiquitin, and a stabilized folding intermediate of apocytochrome b(562) that shows large contributions to (15)N R(1rho) relaxation from chemical exchange.     

Molecular recognition and screening using a 15N group selective STD NMR method

We present a novel saturation transfer difference (STD) experiment where group selective (GS) saturation of amide protons in (15)N labeled hosts is achieved. It is demonstrated that a train of BIRD(d) pulses that inverts only protons attached to (15)N indeed results in saturation of the amide protons, while the background proton magnetization is much less affected. The undesired effect of partial saturation of the unlabeled protons can be completely cancelled out in difference spectra by switching the (15)N carrier between the on- and the off-resonance frequencies. As a result, clean and artifact-free STD spectra are obtained without the need of time-consuming optimization of experimental parameters and acquiring control spectra in the absence of the host. The use of the (15)N-GS STD experiment is demonstrated for the case of a glycopeptide antibiotic (dimeric eremomycin)-cell-wall analogue peptide (N-Ac-D-Ala) model system where the host and guest (1)H signals overlap. The application seems feasible for ligand screening against proteins without the prerequisite of a clean on-resonance frequency or defined ligand library. The new experiment can be used as the basis for studying intermolecular interactions where the standard STD experiment is difficult to optimize.     

Contribution of charged groups to the enthalpic stabilization of the folded states of globular proteins

In this paper we use the results from all-atom molecular dynamics (MD) simulations of proteins and peptides to assess the individual contribution of charged atomic groups to the enthalpic stability of the native state of globular proteins and investigate how the distribution of charged atomic groups in terms of solvent accessibility relates to protein enthalpic stability. The contributions of charged groups is calculated using a comparison of nonbonded interaction energy terms from equilibrium simulations of charged amino acid dipeptides in water (the "unfolded state") and charged amino acids in globular proteins (the "folded state"). Contrary to expectation, the analysis shows that many buried, charged atomic groups contribute favorably to protein enthalpic stability. The strongest enthalpic contributions favoring the folded state come from the carboxylate (COO(-)) groups of either Glu or Asp. The contributions from Arg guanidinium groups are generally somewhat stabilizing, while N(+)(3) groups from Lys contribute little toward stabilizing the folded state. The average enthalpic gain due to the transfer of a methyl group in an apolar amino acid from solution to the protein interior is described for comparison. Notably, charged groups that are less exposed to solvent contribute more favorably to protein native-state enthalpic stability than charged groups that are solvent exposed. While solvent reorganization/release has favorable contributions to folding for all charged atomic groups, the variation in folded state stability among proteins comes mainly from the change in the nonbonded interaction energy of charged groups between the unfolded and folded states. A key outcome is that the calculated enthalpic stabilization is found to be inversely proportional to the excess charge density on the surface, in support of an hypothesis proposed previously.     

Automated NMR assignment of protein side chain resonances using automated projection spectroscopy (APSY)

This paper describes an automated method for sequence-specific NMR assignment of the aliphatic resonances of protein side chains in small- and medium-sized globular proteins in aqueous solution. The method requires the recording of a five-dimensional (5D) automated projection spectroscopy (APSY-) NMR experiment and the subsequent analysis of the APSY peak list with the algorithm ALASCA (Algorithm for local and linear assignment of side chains from APSY data). The 5D APSY-HC(CC-TOCSY)CONH experiment yields 5D chemical shift correlations of aliphatic side chain C-H moieties with the backbone atoms H(N), N, and C'. A simultaneous variation of the TOCSY mixing times and the projection angles in this APSY-type TOCSY experiment gives access to all aliphatic C-H moieties in the 20 proteinogenic amino acids. The correlation peak list resulting from the 5D APSY-HC(CC-TOCSY)CONH experiment together with the backbone assignment of the protein under study is the sole input for the algorithm ALASCA that assigns carbon and proton resonances of protein side chains. The algorithm is described, and it is shown that the aliphatic parts of 17 of the 20 common amino acid side chains are assigned unambiguously, whereas the remaining three amino acids are assigned with a certainty of above 95%. The overall feasibility of the approach is demonstrated with the globular 116-residue protein TM1290, for which reference assignments are known. For this protein, 97% of the expected side chain carbon atoms and 87% of the expected side chain protons were detected with the 5D APSY-HC(CC-TOCSY)CONH experiment in 24 h of spectrometer time, and all these resonances were correctly assigned by ALASCA. Based on the experience with TM1290, we expect that the approach presented in this work is routinely applicable to globular proteins with sizes up to at least 120 amino acids.     

1H-chemical shifts of some dehydro[12]- and dehydro[14]-annulenes

The ring-current (RC) and local anisotropic (LA) contributions to the ¹H-chemical shifts of the dehydro[12]- and dehydro[14]-annulenes 1–13 have been calculated. The calculated shifts are in very good accord with experiment. Only protons with distances <3 Å from a triple bond are obtained at too high a field. It is shown that only the consideration of the combined RC and LA effects can provide an explanation of the chemical shifts of inner and outer protons of annulenes.     

Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy

Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge‐neutral are rare and potentially controversial. Herein, we present a ¹³C‐detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the ¹⁵N^η and ¹⁵N^ϵ chemical shifts of an arginine head group are correlated with that of the directly attached ¹³C^ζ. In the resulting spectrum, the number of protons in the arginine head group can be obtained directly from the ¹⁵N–¹H scalar coupling splitting pattern. We applied this method to unambiguously determine the ionization state of the R52 side chain in the photoactive yellow protein from Halorhodospira halophila . Although only three H^η atoms were previously identified by neutron crystallography, we show that R52 is predominantly protonated in solution.     

Hydrogen-deuterium exchange signature of porcine cerebroside sulfate activator protein

Hydrogen-deuterium exchange can be a sensitive indicator of protein structural integrity. Comparisons were made between cerebroside sulfate activator protein (CSAct) in the native state and after treatment with guanidine hydrochloride plus dithiothreitol. Native protein has three internal disulfide bonds and treated protein has no internal disulfide bonds. The comparisons were made using hydrogen-deuterium exchange measured by electrospray ionization mass spectrometry, percentage alpha-helical content measured by circular dichroism and biological activity measured by the ability to support arylsulfatase A-catalyzed sulfate hydrolysis from cerebroside sulfate. In acidic solvent native protein has 59 exchange refractory protons and treated protein has 20 exchange refractory protons (44 and 14% of the exchangeable proton populations, respectively). In native protein the size of the exchange refractory proton population is sensitive to changes in pH, temperature and the presence of a ligand. It is uninfluenced by the presence or absence of glycosyl groups attached to Asn21. Helical content is virtually identical in native and treated protein. Biological activity is significantly reduced but not obliterated in treated protein. The hydrogen-deuterium exchange profile appears to be a sensitive signature of the correctly folded protein, and reflects a dimension of the protein structure that is not apparent in circular dichroic spectra or in the ability of the protein to support arylsulfatase A-catalyzed sulfate hydrolysis from sulfatide. The hydrogen-deuterium exchange profile will be a valuable criterion for characterizing mutant forms of CSAct produced by recombinant and synthetic paradigms and also the native and mutant forms of related proteins.     

Interaction of single water molecules with silanols in mesoporous silica

Deep Inelastic Neutron Scattering measurements of water confined in mesoporous silica have been carried out. The experiment has been performed at room temperature on dry and on hydrated samples in order to investigate the interaction between the protons and the silanol groups of the confining surface. With this aim we could control the hydration of the pores in such a way as to adsorb 3.0 water molecules per nm(2), corresponding to a 1 to 1 ratio with the silanol groups of the surface. DINS measurements directly measure the mean kinetic energy and the momentum distribution of the protons. A detailed analysis of the hydrated sample has been performed in order to separate the contributions of the protons in the system, allowing us to determine the arrangement of water molecules on the silanol groups. We find that the hydrogen bond of the water proton with the oxygen of the silanol group is much stronger than the hydrogen bonds of bulk water.     

Multiple protonation equilibria in electrostatics of protein-protein binding

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.     

Evidence for slow motion in proteins by multiple refocusing of heteronuclear nitrogen/proton multiple quantum coherences in NMR

A novel NMR method characterizes slow motions in proteins by multiple refocusing of double- and zero-quantum coherences of amide protons and nitrogen-15 nuclei. If both nuclei experience changes in their isotropic chemical shifts because of internal motions on slow time scales (mus - ms), this leads to a difference in the relaxation rates of double- and zero-quantum coherences. This is due to CSM/CSM (chemical shift modulation) cross-correlation effects that are related to the well-known chemical exchange contribution Rex to the decay rate R2 = 1/T2 of nitrogen-15 nuclei. The CSM/CSM contributions can be distinguished from other mechanisms through their dependence on the repetition rate of a Carr-Purcell-Meiboom-Gill (CPMG) multiple refocusing sequence. In ubiquitin, motional processes can be identified that could hitherto not be observed by conventional CPMG nitrogen-15 NMR.     

Optimized measurement temperature gives access to the solution structure of a 49 kDa homohexameric β-propeller

Ph1500 is a homohexameric, two-domain protein of unknown function from the hyperthermophilic archaeon Pyrococcus horikoshii. The C-terminal hexamerization domain (Ph1500C) is of particular interest, as it lacks sequence homology to proteins of known structure. However, it resisted crystallization for X-ray analysis, and proteins of this size (49 kDa) present a considerable challenge to NMR structure determination in solution. We solved the high-resolution structure of Ph1500C, exploiting the hyperthermophilic nature of the protein to minimize unfavorable relaxation properties by high-temperature measurement. Thus, the side chain assignment (97%) and structure determination became possible at full proton density. To our knowledge, Ph1500C is the largest protein for which this has been achieved. To minimize detrimental fast water exchange of amide protons at increased temperature, we employed a strategy where the temperature was optimized separately for backbone and side chain experiments.     

Quantitative Analysis of Spectral Effects due to the Z/E Conformational Equilibria in Derivatives of the Amides and Hydrazides of Dicarboxylic Acids

The contributions from anisotropic magnetic screening and electronic effects to the relative chemical shifts of the NH protons in the amides and N,N-dimethylhydrazides of succinic and glutaric acids were calculated. It was shown that the splitting of the signals of the NH protons is largely determined by the redistribution of electron density in the molecule during the conformational transition.     

Sensitivity enhancement in saturation transfer difference (STD) experiments through optimized excitation schemes

Investigation of ligand-protein interactions by the saturation transfer difference (STD) experiment has been well established in the drug discovery process through numerous examples. Thus, binding epitopes may be mapped by comparing signals of the ligand with and without saturation of the protein. Herein, it is shown that a less selective process allows more protons to assist in the saturation of the protein, thereby considerably enhancing the sensitivity of the STD experiment. Increasing the saturation power entails a greater risk of perturbing the ligand; however, an amplitude modulation of the waveform assists this procedure by distributing the applied energy in sidebands.     

Observation of intermolecular interactions in large protein complexes by 2D-double difference nuclear Overhauser enhancement spectroscopy: application to the 44 kDa interferon-receptor complex

NMR detection of intermolecular interactions between protons in large protein complexes is very challenging because it is difficult to distinguish between weak NOEs from intermolecular interactions and the much larger number of strong intramolecular NOEs. This challenging task is exacerbated by the decrease in signal-to-noise ratio in the often used isotope-edited and isotope-filtered experiments as a result of enhanced T(2) relaxation. Here, we calculate a double difference spectrum that shows exclusively intermolecular NOEs and manifests the good signal-to-noise ratio in 2D homonuclear NOESY spectra even for large proteins. The method is straightforward and results in a complete picture of all intermolecular interactions involving non exchangeable protons. Ninety-seven such (1)H-(1)H NOEs were assigned for the 44 KDa interferon-α2/IFNAR2 complex and used for docking these two proteins. The symmetry of the difference spectrum, its superb resolution, and unprecedented signal-to-noise ratio in this large protein/receptor complex suggest that this method is generally applicable to study large biopolymeric complexes.     

Gas-phase proton-transfer pathways in protonated histidylglycine

Pathways for proton transfer in the histidylglycine cation are examined in the gas-phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero-point energy are included, it is found that all the lowest energy barriers for proton transfer between the N-terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring. In mass spectrometric techniques employing collision-induced dissociation to dissociate protein complex ions or to fragment peptides, these barriers can be overcome, and the protons mobilized. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Multiple molecule effects on the cooperativity of protein folding transitions in simulations

Though molecular simulation of proteins has made notable contributions to the study of protein folding and kinetics, disagreement between simulation and experiment still exists. One of the criticisms levied against simulation is its failure to reproduce cooperative protein folding transitions. This weakness has been attributed to many factors such as a lack of polarizability and adequate capturing of solvent effects. This work, however, investigates how increasing the number of proteins simulated simultaneously can affect the cooperativity of folding transitions--a topic that has received little attention previously. Two proteins are studied in this work: phage T4 lysozyme (Protein Data Bank (PDB) ID: 7LZM) and phage 434 repressor (PDB ID: 1R69). The results show that increasing the number of proteins molecules simulated simultaneously leads to an increase in the macroscopic cooperativity for transitions that are inherently cooperative on the molecular level but has little effect on the cooperativity of other transitions. Taken as a whole, the results identify one area of consideration to improving simulations of protein folding.