Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin

Probing mutation-induced structural perturbations by refinement against residual dipolar couplings: application to the U4 spliceosomal RNP complex

Confident interpretation of biochemical experiments performed with mutated proteins relies on verification of the integrity of the mutant structures. We present a simple and rapid refinement protocol for comparing the structures of mutated and wild-type proteins. Our approach involves measurement of residual dipolar couplings, and only requires assignment of the backbone resonances of the mutant species. We demonstrate application of the protocol to a mutant of the 15.5K protein, a core component of the U4 spliceosomal ribonucleoprotein (RNP) complex. Confirmation of the unperturbed structure of the mutated protein prompted re-examination of a previous mutagenesis study and indicated that the interpretation of mutant binding affinities in terms of direct interfacial contacts should be applied with caution.

A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family

Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using “Backrub” motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

Knowledge of protein properties is essential for enhancing the understanding and engineering of biological functions. One key property of proteins is their flexibility—their intrinsic ability to adopt different conformations. This flexibility can be measured experimentally but the measurements are indirect and computational models are required to interpret them. Here we develop a new computational method for interpreting these measurements of flexibility and use it to create a model of flexibility of the protein ubiquitin. We apply our results to show relationships between the flexibility of one protein and the diversity of structures and amino acid sequences of the protein's evolutionary family. Thus, our results show that more accurate computational modeling of protein flexibility is useful for improving prediction of a broader range of amino acid sequences compatible with a given protein. Our method will be helpful for advancing methods to rationally engineer protein functions by enabling sampling of conformational and sequence diversity similar to that of a protein's evolutionary family.

Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR

Nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) provide a unique opportunity for spatially characterizing complex motions in biomolecules with time scale sensitivity extending up to milliseconds. Up to five motionally averaged Wigner rotation elements, (D(0k)2(alphaalpha)), can be determined experimentally using RDCs measured in five linearly independent alignment conditions and applied to define motions of axially symmetric bond vectors. Here, we show that up to 25 motionally averaged Wigner rotation elements, (D(mk)2(alphabetagamma)), can be determined experimentally from multialignment RDCs and used to characterize rigid-body motions of chiral domains. The 25 (D(mk)2(alphabetagamma)) elements form a basis set that allows one to measure motions of a domain relative to an isotropic distribution of reference frames anchored on a second domain (and vice versa), thus expanding the 3D spatial resolution with which motions can be characterized. The 25 (D(mk)2(alphabetagamma)) elements can also be used to fit an ensemble consisting of up to eight equally or six unequally populated states. For more than two domains, changing the identity of the domain governing alignment allows access to new information regarding the correlated nature of the domain fluctuations. Example simulations are provided that validate the theoretical derivation and illustrate the high spatial resolution with which rigid-body domain motions can be characterized using multialignment and multireference RDCs. Our results further motivate the development of experimental approaches for both modulating alignment and anchoring it on specifically targeted domains.

Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement

Many biological macromolecular interactions proceed via lowly-populated, highly transient species that arise from rare excursions between the minimum free energy configuration and other local minima of the free energy landscape. Little is known about the structural properties of such lowly-occupied states since they are difficult to trap and hence inaccessible to conventional structural and biophysical techniques. Yet these states play a crucial role in a variety of dynamical processes including molecular recognition and binding, allostery, induced-fit and self-assembly. Here we highlight recent progress in paramagnetic nuclear magnetic resonance to detect, visualize and characterize lowly-populated transient species at equilibrium. The underlying principle involves the application of paramagnetic relaxation enhancement (PRE) in the fast exchange regime. Under these conditions the footprint of the minor species can be observed in the PRE profiles measured for the major species, providing distances between the paramagnetic label and protons of interest are shorter in the minor species than the major one. Ensemble simulated annealing refinement directly against the PRE data permits one to obtain structural data on the minor species. We have used the PRE (a) to detect and characterize the stochastic target search process whereby a sequence-specific transcription factor (the Hox-D9 homeodomain) binds to non-cognate DNA sites as a means of enhancing the rate of specific association via intramolecular sliding and intermolecular translocation; (b) to directly visualize the distribution of non-specific transient encounter complexes involved in the formation of stereospecific protein-protein complexes; (c) to detect and visualize ultra-weak self-association of a protein, a process that is relevant to early nucleation events involved in the formation of higher order structures; and (d) to determine the structure of a minor species for a multidomain protein (maltose binding protein) where large interdomain motions are associated with ligand binding, thereby shedding direct light on the fundamental question of allostery versus induced fit in this system. The PRE offers unique opportunities to directly probe and explore in structural terms lowly-populated regions of the free energy landscape and promises to yield fundamental new insights into biophysical processes.

Mechanism of partial agonism at the GluR2 AMPA receptor: Measurements of lobe orientation in solution

The mechanism by which the binding of a neurotransmitter to a receptor leads to channel opening is a central issue in molecular neurobiology. The structure of the agonist binding domain of ionotropic glutamate receptors has led to an improved understanding of the changes in structure that accompany agonist binding and have provided important clues about the link between these structural changes and channel activation and desensitization. However, because the binding domain has exhibited different structures under different crystallization conditions, understanding the structure in the absence of crystal packing is of considerable importance. The orientation of the two lobes of the binding domain in the presence of a full agonist, an antagonist, and several partial agonists was measured using NMR spectroscopy by employing residual dipolar couplings. For some partial agonists, the solution conformation differs from that observed in the crystal. A model of channel activation based on the results is discussed.

Tyr130 phosphorylation triggers Syk release from antigen receptor by long-distance conformational uncoupling

The Syk protein-tyrosine kinase plays a major role in signaling through the B cell receptor for antigen (BCR). Syk binds the receptor via its tandem pair of SH2 domains interacting with a doubly phosphorylated immunoreceptor tyrosine-based activation motif (dp-ITAM) of the BCR complex. Upon phosphorylation of Tyr-130, which lies between the two SH2 domains distant to the phosphotyrosine binding sites, Syk dissociates from the receptor. To understand the structural basis for this dissociation, we investigated the structural and dynamic characteristics of the wild type tandem SH2 region (tSH2) and a variant tandem SH2 region (tSH2(pm)) with Tyr-130 substituted by Glu to permanently introduce a negative charge at this position. NMR heteronuclear relaxation experiments, residual dipolar coupling measurements and analytical ultracentrifugation revealed substantial differences in the hydrodynamic behavior of tSH2 and tSH2(pm). Although the two SH2 domains in tSH2 are tightly associated, the two domains in tSH2(pm) are partly uncoupled and tumble in solution with a faster correlation time. In addition, the equilibrium dissociation constant for the binding of tSH2(pm) to dp-ITAM (1.8 microM) is significantly higher than that for the interaction between dp-ITAM and tSH2 but is close to that for a singly tyrosine-phosphorylated peptide binding to a single SH2 domain. Experimental data and hydrodynamic calculations both suggest a loss of domain-domain contacts and change in relative orientation upon the introduction of a negative charge on residue 130. A long-distance structural mechanism by which the phosphorylation of Y130 negatively regulates the interaction of Syk with immune receptors is proposed.

Structure, function, and evolution of bacterial ATP-binding cassette systems

SUMMARY

ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.

Rigid body essential X-ray crystallography: distinguishing the bend and twist of glutamate receptor ligand binding domains

The ligand-binding domain (LBD) from the ionotropic glutamate receptor subtype 2 (GluR2) has been shown to adopt a range of ligand-dependent conformational states. These states have been described in terms of the rotation required to fit subdomain (lobe) 2 following superposition of subdomain (lobe) 1. The LBD has a closed-cleft conformation for full agonists, but partial agonists induce a range of closure, which in turn controls the open probability of discrete subconductance states in the full-length receptor. Although this description is useful, it may not account for all physiologically important motions that the receptor undergoes. We have used an approach that combines the methods of essential dynamics and rigid-body dynamics to analyze 124 monomer domains from 55 crystal structures of the GluR2 LBD. We are able to show that partial agonists also induce a significant amount of twist that would not be anticipated using one rotational descriptor between apo and full-agonist-bound states. Furthermore, one of the crystal structures (chain B from 1P1U, the GluR2 L650T-AMPA complex), which has been suggested to represent an agonist-bound inactive form of the receptor, lies at the extreme of this twist motion. We suggest that partial agonists not only prevent full closure but also move the receptor closer to this inactive state. We demonstrate additionally how the method can be used to compare the results of molecular dynamics simulations with the crystallographic data and the extent to which the conformational space explored by both overlaps.

De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media

The straightforward interpretation of solution state residual dipolar couplings (RDCs) in terms of internuclear vector orientations generally requires prior knowledge of the alignment tensor, which in turn is normally estimated using a structural model. We have developed a protocol which allows the requirement for prior structural knowledge to be dispensed with as long as RDC measurements can be made in three independent alignment media. This approach, called Rigid Structure from Dipolar Couplings (RSDC), allows vector orientations and alignment tensors to be determined de novo from just three independent sets of RDCs. It is shown that complications arising from the existence of multiple solutions can be overcome by careful consideration of alignment tensor magnitudes in addition to the agreement between measured and calculated RDCs. Extensive simulations as well applications to the proteins ubiquitin and Staphylococcal protein GB1 demonstrate that this method can provide robust determinations of alignment tensors and amide N-H bond orientations often with better than 10 degrees accuracy, even in the presence of modest levels of internal dynamics.

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in which the closed state is energetically inaccessible and interdomain rearrangement is induced by ligand or substrate binding, or whether the predominantly open form already coexists in rapid equilibrium with a minor closed species. The maltose-binding protein (MBP), a member of the bacterial periplasmic binding protein family, provides a model system for investigating this problem because it has been the subject of extensive studies by crystallography, NMR and other biophysical techniques. Here we show that although paramagnetic relaxation enhancement (PRE) data for the sugar-bound form are consistent with the crystal structure of holo MBP, the PRE data for the apo state are indicative of a rapidly exchanging mixture (ns to mus regime) of a predominantly ( approximately 95%) open form (represented by the apo crystal structure) and a minor (approximately 5%) partially closed species. Using ensemble simulated annealing refinement against the PRE data we are able to determine a <r(-6)> ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state.

NMR identification of transient complexes critical to adenylate kinase catalysis

A fundamental question in protein chemistry is how the native energy landscape of enzymes enables efficient catalysis of chemical reactions. Adenylate kinase is a small monomeric enzyme that catalyzes the reversible conversion of AMP and ATP into two ADP molecules. Previous structural studies have revealed that substrate binding is accompanied by large rate-limiting spatial displacements of both the ATP and AMP binding motifs. In this report a solution-state NMR approach was used to probe the native energy landscape of adenylate kinase in its free form, in complex with its natural substrates, and in the presence of a tight binding inhibitor. Binding of ATP induces a dynamic equilibrium in which the ATP binding motif populates both the open and the closed conformations with almost equal populations. A similar scenario is observed for AMP binding, which induces an equilibrium between open and closed conformations of the AMP binding motif. These ATP- and AMP-bound structural ensembles represent complexes that exist transiently during catalysis. Simultaneous binding of AMP and ATP is required to force both substrate binding motifs to close cooperatively. In addition, a previously unknown unidirectional energetic coupling between the ATP and AMP binding sites was discovered. On the basis of these and previous results, we propose that adenylate kinase belongs to a group of enzymes whose substrates act to shift pre-existing equilibria toward catalytically active states.

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

We present a protocol for determining the relative orientation and dynamics of A-form helices in 13C/15N isotopically enriched RNA samples using NMR residual dipolar couplings (RDCs). Non-terminal Watson-Crick base pairs in helical stems are experimentally identified using NOE and trans-hydrogen bond connectivity and modeled using the idealized A-form helix geometry. RDCs measured in the partially aligned RNA are used to compute order tensors describing average alignment of each helix relative to the applied magnetic field. The order tensors are translated into Euler angles defining the average relative orientation of helices and order parameters describing the amplitude and asymmetry of interhelix motions. The protocol does not require complete resonance assignments and therefore can be implemented rapidly to RNAs much larger than those for which complete high-resolution NMR structure determination is feasible. The protocol is particularly valuable for exploring adaptive changes in RNA conformation that occur in response to biologically relevant signals. Following resonance assignments, the procedure is expected to take no more than 2 weeks of acquisition and data analysis time.

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein's rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning are also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of a Lys48-linked diubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution.

A model of interdomain mobility in a multidomain protein

Domain mobility plays an essential role in the biological function of multidomain systems. The characteristic times of domain motions fall into the interval from nano- to milliseconds, amenable to NMR studies. Proper analysis of NMR relaxation data for these systems in solution has to account for interdomain motions, in addition to the overall tumbling and local intradomain dynamics. Here we propose a model of interdomain mobility in a multidomain protein, which considers domain reorientations as exchange/interconversion between two distinct conformational states of the molecule, combined with fully anisotropic overall tumbling. Analysis of 15N-relaxation data for Lys48-linked diubiquitin at pH 4.5 and 6.8 showed that this model adequately fits the experimental data and allows characterization of both structural and motional properties of diubiquitin, thus providing information about the relative orientation of ubiquitin domains in both interconverting states. The analysis revealed that the two domains reorient on a time scale of 9-30 ns, with the amplitudes sufficient for allowing a protein ligand access to the binding sites sequestered at the interface in the closed conformation. The analysis of a possible mechanism controlling the equilibrium between the interconverting states in diubiquitin points toward protonation of His68, which results in three different charged states of the molecule, with zero, +e, and +2e net charge. Only two of the three states are noticeably populated at pH 4.5 or 6.8, which assures applicability of the two-state model to diubiquitin at these conditions. We also compare our model with the "extended model-free" approach and discuss possible future developments of the model.

A new strategy for structure determination of large proteins in solution without deuteration

So far high-resolution structure determination by nuclear magnetic resonance (NMR) spectroscopy has been limited to proteins <30 kDa, although global fold determination is possible for substantially larger proteins. Here we present a strategy for assigning backbone and side-chain resonances of large proteins without deuteration, with which one can obtain high-resolution structures from (1)H-(1)H distance restraints. The strategy uses information from through-bond correlation experiments to filter intraresidue and sequential correlations from through-space correlation experiments, and then matches the filtered correlations to obtain sequential assignment. We demonstrate this strategy on three proteins ranging from 24 to 65 kDa for resonance assignment and on maltose binding protein (42 kDa) and hemoglobin (65 kDa) for high-resolution structure determination. The strategy extends the size limit for structure determination by NMR spectroscopy to 42 kDa for monomeric proteins and to 65 kDa for differentially labeled multimeric proteins without the need for deuteration or selective labeling.

Analysis of interdomain dynamics in a two-domain protein using residual dipolar couplings together with 15N relaxation data

In this paper, we propose the idea that simultaneous analysis of NMR relaxation data and residual dipolar couplings (RDCs) can provide information about interdomain dynamics in a multidomain protein, which cannot be derived from each data set separately. Specifically, such an approach can be useful when the interdomain motions occur on a timescale comparable to or slower than the overall tumbling in solution. We analyze residual dipolar couplings together with 15N relaxation data for Lys48-linked di-ubiquitin (Ub2), in which interdomain dynamics are described as interconversion between two distinct conformational states of the protein. Our results show that 15N relaxation and residual dipolar coupling data can be used as two complementary experimental data sets for consistent characterization of interdomain conformations and dynamics in this dual-domain protein.

Inter-domain orientation and motions in VAT-N explored by residual dipolar couplings and 15N backbone relaxation

The N-terminal domain of VAT (Valosine-containing protein-like ATPase of Thermoplasma acidophilum), VAT-N (20.5 kDa), is considered to be the primary substrate-recognition site of the complex. The solution structure of VAT-N derived in our laboratory using conventionally obtained NMR restraints shows the existence of two equally sized sub-domains, VAT-Nn and VAT-Nc, together forming a kidney-shaped overall structure. The putative substrate-binding site of VAT-N involves free loops and a highly charged groove located on the surface of the protein. Alternatively, the opening of the cleft between the domains to accommodate substrate has been proposed to be part of the functional mechanism. We have used the residual dipolar couplings (RDCs) obtained in a bicelle medium to refine the structure of VAT-N. The long-range information available from RDCs both defines the sub-domain orientation and probes possible inter-domain motions. In addition, 15N backbone relaxation data were obtained and analysed within the model-free framework. Together, the data provides a refined structure with improved local geometry, but with the overall kidney shape intact. Further, the protein is rigid overall, with no evidence of inter-domain motions.

Interdomain mobility in di-ubiquitin revealed by NMR

Domain orientation and dynamics can play an essential role in the function of multidomain proteins. Lys48-linked polyubiquitin chains, the principal signal for proteasomal protein degradation, adopt a closed conformation at physiological conditions, in which the functionally important residues Leu8, Ile44, and Val70 are sequestered at the interdomain interface. This interface must open in order for these groups to become available for interactions with various chain-recognition factors. Knowledge of the mechanism of domain motion leading to the opening of the interdomain interface in polyubiqutin is, therefore, essential for the understanding of the processes controlling molecular recognition events in polyubiquitin signaling. Here we use NMR to characterize the interdomain dynamics that open the interface in a di-ubiquitin chain. This process occurs via domain reorientations on a 10-ns time scale and with the amplitudes that are sufficient for making functionally important hydrophobic residues in polyubiquitin available for direct interactions with various ubiquitin-binding factors. The analysis revealed the structures of the interconverting conformational states of di-ubiquitin and the rates and amplitudes of this process at near-physiological and acidic pH. The proposed mechanism of domain reorientation is quite general and could serve as a paradigm of interdomain mobility in other multidomain systems.

A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints

We present a novel target function based on atomic coordinates that permits quaternary structural refinement of multi-domain protein-protein or protein-RNA complexes. It requires that the high-resolution structures of the individual domains are known and that small angle scattering (SAS) data as well as NMR orientational restraints from residual dipolar couplings (RDCs) of the complex are available. We show that, when used in combination, the translational and rotational restraints contained in SAS intensities and RDCs, respectively, define a target potential function that permits to determine the overall topology of complexes made up of domains with low internal symmetry. We apply the target function on a modestly anisotropic model system, the Barnase/Barstar complex, and discuss factors that influence the structural refinement such as data errors and the geometrical properties of the individual domains.

NMR solution structure of the tandem Src homology 3 domains of p47phox complexed with a p22phox-derived proline-rich peptide

The phagocyte NADPH oxidase plays a crucial role in host defense against microbial infections by generating reactive oxygen species. It is a multisubunit enzyme composed of membrane-bound flavocytochrome b558 as well as cytosolic components, including p47phox, which is essential for assembly of the complex. When phagocytes are activated, the cytosolic components of the NADPH oxidase translocate to flavocytochrome b558 due to binding of the tandem Src homology 3 (SH3) domains of p47phox to a proline-rich region in p22phox, a subunit of flavocytochrome b558. Using NMR titration, we first identified the proline-rich region of p22phox that is essential for binding to the tandem SH3 domains of p47phox. We subsequently determined the solution structure of the p47phox tandem SH3 domains complexed with the proline-rich peptide of p22phox using NMR spectroscopy. In contrast to the intertwined dimer reported for the crystal state, the solution structure is a monomer. The central region of the p22phox peptide forms a polyproline type II helix that is sandwiched by the N- and C-terminal SH3 domains, as was observed in the crystal structure, whereas the C-terminal region of the peptide takes on a short alpha-helical conformation that provides an additional binding site with the N-terminal SH3 domain. Thus, the C-terminal alpha-helical region of the p22phox peptide increases the binding affinity for the tandem SH3 domains of p47phox more than 10-fold.

Estimating the accuracy of protein structures using residual dipolar couplings

It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H-15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable R values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable R values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.

Various strategies of using residual dipolar couplings in NMR-driven protein docking: Application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data

When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution structures of the free molecules, to model the structure of a complex in solution based solely on chemical shift perturbation (CSP) data in combination with orientational restraints from residual dipolar couplings (RDCs) when available. RDCs can be incorporated into the docking following various strategies: as direct restraints and/or as intermolecular intervector projection angle restraints (Meiler et al., J Biomol NMR 2000;16:245-252). The advantage of the latter for docking is that they directly define the relative orientation of the molecules. A combined protocol in which RDCs are first introduced as intervector projection angle restraints and at a later stage as direct restraints is shown here to give the best performance. This approach, implemented in our information-driven docking approach HADDOCK (Dominguez et al., J Am Chem Soc 2003;125:1731-1737), is used to determine the solution structure of the Lys48-linked di-ubiquitin, for which chemical shift mapping, RDCs, and (15)N-relaxation data have been previously obtained (Varadan et al., J Mol Biol 2002;324:637-647). The resulting structures, derived from CSP and RDC data, are cross-validated using (15)N-relaxation data. The solution structure differs from the crystal structure by a 20 degrees rotation of the two ubiquitin units relative to each other.

A structural model for the membrane-bound form of the juxtamembrane domain of the epidermal growth factor receptor

The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family involved in the regulation of cellular proliferation and differentiation. Its juxtamembrane domain (JX), the region located between the transmembrane and kinase domains, plays important roles in receptor trafficking. Two sorting signals, a PXXP motif and a 658LL659 motif, are responsible for basolateral sorting in polarized epithelial cells, and a 679LL680 motif targets the ligand-activated receptor for lysosomal degradation. To understand the regulation of these signals, we characterized the structural properties of recombinant JX domain in aqueous solution and in dodecylphosphocholine (DPC) detergent. JX is inherently unstructured in aqueous solution, albeit a nascent helix encompasses the lysosomal sorting signal. In DPC micelles, structures derived from NMR data showed three amphipathic, helical segments. A large, internally inconsistent group of long range nuclear Overhauser effects suggest a close proximity of the helices, and the presence of significant conformational averaging. Models were determined for the average JX conformation using restraints representing the translational restriction due to micelle-surface adsorption, and the helix orientations were determined from residual dipolar couplings. Two equivalent average structural models were obtained that differ only in the relative orientation between first and second helices. In these models, the 658LL659 and 679LL680 motifs are located in the first and second helices and face the micelle surface, whereas the PXXP motif is located in a flexible helix-connecting region. The data suggest that the activity of these signals may be regulated by their membrane association and restricted accessibility in the intact receptor.

NMR studies of protein structure and dynamics

Recent advances in solution NMR spectroscopy have significantly extended the spectrum of problems that can now be addressed with this technology. In particular, studies of proteins with molecular weights on the order of 100 kDa are now possible at a level of detail that was previously reserved for much smaller systems. An example of the sort of information that is now accessible is provided in a study of malate synthase G, a 723 residue enzyme that has been a focal point of research efforts in my laboratory. Details of the labeling schemes that have been employed and optimal experiments for extraction of structural and dynamics information on this protein are described. NMR studies of protein dynamics, in principle, give insight into the relation between motion and function. A description of deuterium-based spin relaxation methods for the investigation of side chain dynamics is provided. Examples where millisecond (ms) time scale dynamics play an important role and where relaxation dispersion NMR spectroscopy has been particularly informative, including applications involving the membrane enzyme PagP and mutants of the Fyn SH3 domain that fold on a ms time scale, are presented.

Protein backbone dynamics from N-HN dipolar couplings in partially aligned systems: a comparison of motional models in the presence of structural noise

Residual dipolar couplings (RDCs) provide excellent probes for the exploration of dynamics in biomolecules on biologically relevant time-scales. Applying geometric motional models in combination with high-resolution structures to fit experimental RDCs allows the extraction of local dynamic amplitudes of peptide planes in proteins using only a limited number of data points. Here we compare the behaviour of three simple and intuitive dynamic modes: the Gaussian axial fluctuation model (1D-GAF), the two-site jump model, and a model supposing axially symmetric motion about a mean orientation. The requirement of a structural model makes this kind of methodology potentially very sensitive to structural imprecision. Numerical simulations of RDC dynamic averaging under different regimes show that the anisotropic motional models are more geometrically stringent than the axially symmetric model making it more difficult to alias structural noise as artificial dynamic amplitudes. Indeed, it appears that the model extracts accurate motional amplitudes even in the presence of significant structural error. We also show that a two-site jump model, also assuming the (alpha)C(i-1)-(alpha)C(i) as rotation axis, can only be distinguished from the previously developed GAF model beyond amplitude/jumps of around 40 degrees. The importance of appropriate estimation of the molecular alignment tensor for determination of local motional amplitudes is also illustrated here. We demonstrate a systematic scaling of extracted dynamic amplitudes if a static structure is assumed when determining the alignment tensor from dynamically averaged RDCs. As an example an artificial increase of 0.14 (0.85 compared to the expected 0.71) is observed in the extracted S2 if a pervasive 20 degrees GAF motion is present that is ignored in the tensor determination. Finally we apply a combined approach using the most appropriate motional model, to complete the analysis of dynamic motions from protein G.

Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins

A chemical genetics approach to functional analysis of gene products utilizes high-throughput target-based screens of compound libraries to identify ligands that modulate the activity of proteins of interest. Candidates are further screened using functional assays designed specifically for the protein--and function--of interest, suffering from the need to customize the assay to each protein. An alternative strategy is to utilize a probe to detect the structural changes that usually accompany binding of a functional ligand. Wide-angle X-ray scattering from proteins provides a means to identify a broad range of ligand-induced changes in secondary, tertiary, and quaternary structure. The speed and accuracy of data acquisition, combined with the label-free targets and binding conditions achievable, indicate that WAXS is well suited as a moderate-throughput assay in the detection and analysis of protein-ligand interactions.

Structure determination of large biological RNAs

Complex RNA structures regulate many biological processes but are often too large for structure determination by nuclear magnetic resonance (NMR) methods. We determined the solution structure of domain II of the hepatitis C viral internal ribosome entry site (HCV IRES), a 25-kDa RNA, using a novel NMR approach. Conventional short-range, distance, and torsion angle NMR restraints were combined with long-range, angular restraints derived from residual dipolar couplings (RDCs) to improve both the local and global precision of the structure. This powerful approach should be generally applicable to the NMR structure determination of large, modular RNAs.

Determination of helical membrane protein topology using residual dipolar couplings and exhaustive search algorithm: application to phospholamban

Dipolar waves are distinct hallmarks of both the secondary and tertiary structures of alpha-helical proteins that are immobilized in membrane bilayers or embedded in anisotropic media. We present a simple, semi-empirical approach that exploits the modulation of the amplitude and average of dipolar waves to determine the topology of alpha-helical proteins. Moreover, we describe the application of this method for the structural determination of a detergent solubilized membrane protein, phospholamban (PLB) that is involved in calcium regulation of cardiac muscle. When combined with high-resolution solid-state NMR data, this method can serve as a fast route for determining the topology of helical membrane proteins solubilized in detergent micelles.

Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins

Recent developments in NMR spectroscopy, which include new experiments that increase the lifetimes of NMR signals or that precisely define the orientation of internuclear bond vectors with respect to a common molecular frame, have significantly increased the size of proteins for which quantitative structural and dynamic information can be obtained. These experiments have, in turn, benefited from new labeling strategies that continue to drive the field. The utility of the new methodology is illustrated by considering applications to malate synthase G, a 723 residue enzyme, which is the largest single polypeptide chain for which chemical shift assignments have been obtained to date. New experiments developed specifically to address the complexity and low sensitivity of spectra recorded on this protein are presented. A discussion of the chemical information that is readily available from studies of systems in the 100 kDa mol wt range is included. Prospects for membrane protein structure determination are discussed briefly in the context of an application to an Escherichia coli enzyme, PagP, localized to the outer membrane of gram-negative bacteria.

Residual dipolar couplings in NMR structure analysis

Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide long-range orientational information. RDCs are now widely utilized in structure calculations. Increasingly, they are being used in novel applications to address complex issues in structural biology such as the accurate determination of the global structure of oligonucleotides and the relative orientation of protein domains. This review briefly describes the theory and methods for obtaining RDCs and then describes the range of biological applications where RDCs have been used.

Solution Structure of the Tandem Src Homology 3 Domains of p47 in an Autoinhibited Form

The phagocyte NADPH oxidase is a multisubunit enzyme responsible for the generation of superoxide anions (O(2).) that kill invading microorganisms. p47(phox) is a cytosolic subunit of the phagocyte NADPH oxidase, which plays a crucial role in the assembly of the activated NADPH oxidase complex. The molecular shapes of the p47(phox) tandem SH3 domains either with or without a polybasic/autoinhibitory region (PBR/AIR) at the C terminus were studied using small angle x-ray scattering. The tandem SH3 domains with PBR/AIR formed a compact globular structure, whereas the tandem SH3 domains lacking the PBR/AIR formed an elongated structure. Alignment anisotropy analysis by NMR based on the residual dipolar couplings revealed that the tandem SH3 domains with PBR/AIR were in good agreement with a globular module corresponding to the split half of the intertwisted dimer in crystalline state. The structure of the globular module was elucidated to represent a solution structure of the tandem SH3 domain in the autoinhibited form, where the PBR/AIR bundled the tandem SH3 domains and the linker forming a closed structure. Once PBR/AIR is released by phosphorylation, rearrangements of the SH3 domains may occur, forming an open structure that binds to the cytoplasmic proline-rich region of membrane-bound p22(phox).

How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?

The magnitude of backbone internal motions in the small protein ubiquitin that needs to be invoked to account for dipolar coupling data measured in multiple alignment media is investigated using an intuitively straightforward approach. This involves simultaneous refinement of the coordinates (against NOE, torsion angle, and dipolar coupling restraints) and optimization of the magnitudes and orientations of the alignment tensors by means of torsion angle simulated annealing and Cartesian space minimization. We show that N-H dipolar couplings in 11 different alignment media and N-C', H(N)-C', and C alpha-C' dipolar coupling in two alignment media can be accounted for, at approximately the level of uncertainty in the experimental data, by a single structure representation. Extension to a two-member ensemble representation which provides the simplest description of anisotropic motions in the form of a two-site jump model (in which the overall calculated dipolar couplings are the averages of the calculated dipolar couplings of the individual ensemble members), results in modest, but significant, improvements in dipolar coupling R-factors for both the working set of couplings used in the refinement and for the free cross-validated set of C alpha-H alpha dipolar couplings recorded in two alignment media. Extensions to larger ensemble sizes do not result in any R-factor improvement for the cross-validated C alpha-H alpha dipolar couplings. With a few notable exceptions, the amplitudes of the anisotropic motions are small, with S(2)(jump) order parameters > or =0.8. Moreover, the structural impact of those few residues that do exhibit larger amplitude motions (S(2)(jump) ranging from 0.3 to 0.8) is minimal and can readily be accommodated by very small backbone atomic rms shifts (<0.5 A) because of compensatory changes in phi and psi backbone torsion angles. In addition, evidence for correlated motions of N-H bond vectors is observed. For most practical applications, however, refinement of NMR structures against dipolar couplings using a single structure representation is adequate and will not adversely impact coordinate accuracy within the limits of the NMR method.

Experimentally exploring the conformational space sampled by domain reorientation in calmodulin

The conformational space sampled by the two-domain protein calmodulin has been explored by an approach based on four sets of NMR observables obtained on Tb(3+)- and Tm(3+)-substituted proteins. The observables are the pseudocontact shifts and residual dipolar couplings of the C-terminal domain when lanthanide substitution is at the N-terminal domain. Each set of observables provides independent information on the conformations experienced by the molecule. It is found that not all sterically allowed conformations are equally populated. Taking the N-terminal domain as the reference, the C-terminal domain preferentially resides in a region of space inscribed in a wide elliptical cone. The axis of the cone is tilted by approximately 30 degrees with respect to the direction of the N-terminal part of the interdomain helix, which is known to have a flexible central part in solution. The C-terminal domain also undergoes rotation about the axis defined by the C-terminal part of the interdomain helix. Neither the extended helix conformation initially observed in the solid state for free calcium calmodulin nor the closed conformation(s) adopted by calcium calmodulin either alone or in its adduct(s) with target peptide(s) is among the most preferred ones. These findings are unique, both in terms of structural information obtained on a biomolecule that samples multiple conformations and in terms of the approach developed to achieve the results. The same approach is in principle applicable to other multidomain proteins, as well as to multiple interaction modes between two macromolecular partners.

REDCAT: a residual dipolar coupling analysis tool

Recent advancements in the utilization of residual dipolar couplings (RDCs) as a means of structure validation and elucidation have demonstrated the need for, not only a more user friendly, but also a more powerful RDC analysis tool. In this paper, we introduce a software package named REsidual Dipolar Coupling Analysis Tool (REDCAT) designed to address the above issues. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk, which is highly portable. Furthermore, the computational engine behind this GUI is written in C/C++ and its computational performance is therefore excellent. The modular implementation of REDCAT's algorithms, with separation of the computational engine from the graphical engine allows for flexible and easy command line interaction. This feature can be utilized for the design of automated data analysis sessions. Furthermore, this software package is portable to Linux clusters for high throughput applications. In addition to basic utilities to solve for order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is under-determined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging processes.

Emerging structural explanations of ionotropic glutamate receptor function

High-resolution studies of ionotropic glutamate receptor (iGluR) extracellular domains are beginning to bridge the gap between structure and function. Crystal structures have defined the ligand binding pocket well beyond what was suggested by mutational analysis and homology models alone, providing initial suggestions about the mechanisms of channel gating and desensitization. NMR-derived backbone dynamics and molecular dynamics simulations have added further insights into the role of protein dynamics in receptor function. As a whole, the current knowledge of iGluR structure in conjunction with new advances in the understanding of K+ channels provides a vastly improved understanding of iGluR function. This review focuses on structural and dynamic studies of the extracellular ligand binding domain of iGluRs and the pore region of K+ channels that have contributed to mechanistic insights into the processes of iGluR gating and desensitization

Ionotropic Glutamate Receptor Recognition and Activation

Ionotropic glutamate receptors are the major excitatory neurotransmitters in mammalian brain but are found throughout the animal kingdom as well as in plants and bacteria. A great deal of progress in understanding the structure of these essential neurotransmitter receptors has been made since the first examples were cloned and sequenced in 1989. The atomic structure of the ligand-binding domain of several ionotropic glutamate receptors has been determined, and a great deal of progress has been made in relating the structural properties of the binding site to the function of the intact receptor. In addition, the identification of glutamate receptors from a wide variety of organisms ranging from several types of bacteria to Arabidopsis to a range of animal species has made glutamate receptors a molecular laboratory for studying the evolution of proteins. The fact that glutamate receptors are a particularly ancient intercellular signaling molecule suggests a potential role in the transition from single celled to multicellular organisms. This review focuses on the structure and dynamics of ionotropic glutamate receptors and their relation to the function and evolution of these proteins.

Crystal environments probed by EPR spectroscopy. Variations in the EPR spectra of Co(II)(octaethylporphyrin) doped in crystalline diamagnetic hosts and a reassessment of the electronic structure of four-coordinate cobalt(II)

The powder and single-crystal EPR spectra of Co(II)(OEP) (OEP is the dianion of octaethylporphyrin) doped into a range of diamagnetic crystals including simple four-coordinate hosts, H(2)(OEP), the triclinic B form of Ni(II)(OEP), the tetragonal form of Ni(II)(OEP) and Zn(II)(OEP); five-coordinate hosts, micro-dioxane)[Zn(II)(OEP)](2) and (py)Zn(II)(OEP); six-coordinate hosts, (py)(2)Zn(II)(OEP) and (py)(2)Mg(II)(OEP); and hosts containing fullerenes, C(60).2Zn(II)(OEP).CHCl(3), C(70).Ni(II)(OEP).C(6)H(6).CHCl(3), and C(60).Ni(II)(OEP).2C(6)H(6) have been obtained and analyzed. Spectra were simulated using a program that employed the exact diagonalization of the 16 x 16 complex spin Hamiltonian matrix. The EPR spectra of these doped samples are very sensitive to the environment within each crystal with the crystallographic site symmetry determining whether axial or rhombic resonance patterns are observed. For Co(II)(OEP) doped into tetragonal Ni(II)(OEP) (which displays a very large g( perpendicular ) of 3.405 and a very small g( parallel ) of 1.544) and several other crystals containing four-coordinate metal sites, the g components could not be fit using existing theory with the assumption of the usual z(2) ground state. However, reasonable agreement of the observed EPR parameters could be obtained by assuming that the unpaired electron resides in an xy orbital in the four-coordinate complexes.

The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy

Maltose-binding protein (MBP) is a two-domain protein that undergoes a ligand-mediated conformational rearrangement from an "open" to a "closed" structure on binding to maltooligosaccharides. To characterize the energy landscape associated with this transition, we have generated five variants of MBP with mutations located in the hinge region of the molecule. Residual dipolar couplings, measured in the presence of a weak alignment medium, have been used to establish that the average structures of the mutant proteins are related to each other by domain rotation about an invariant axis, with the rotation angle varying from 5 degrees to 28 degrees. Additionally, the domain orientations observed in the wild-type apo and ligand-bound (maltose, maltotriose, etc.) structures are related through a rotation of 35 degrees about the same axis. Remarkably, the free energy of unfolding, measured by equilibrium denaturation experiments and monitored by fluorescence spectroscopy, shows a linear correlation with the rotation angle, with the stability of the (apo)protein decreasing with domain closure by 212 +/- 16 cal mol-1 per degree of rotation. The apparent binding energy for maltose also shows a similar correlation with the interdomain angle, suggesting that the mutations, as they relate to binding, affect predominantly the ligand-free structure. The linearity of the energy change is interpreted in terms of an increase in the extent of hydrophobic surface that becomes solvent accessible on closure. The combination of structural, stability, and binding data allows separation of the energetics of domain reorientation from ligand binding. This work presents a near quantitative structure-energy-binding relationship for a series of mutants of MBP, illustrating the power of combined studies involving protein engineering and solution NMR spectroscopy.

Theoretical Analysis of Residual Dipolar Coupling Patterns in Regular Secondary Structures of Proteins

A new approach to the interpretation of residual dipolar couplings for the regular secondary structures of proteins is presented. This paper deals with the analysis of the steric and chiral requirements of protein secondary structures and establishes a quantitative correlation between structure periodicity and the experimental values of the backbone residual dipolar couplings. Building on the recent interpretation of the periodicity of residual dipolar couplings in alpha-helices (i.e., "dipolar waves"), a general parametric equation for fitting the residual dipolar couplings of any regular secondary structure is derived. This equation interprets the modulation of the residual dipolar couplings' periodicity in terms of the secondary structure orientation with respect to an arbitrary reference frame, laying the groundwork for using backbone residual dipolar couplings as a fast tool for determining protein folding by NMR spectroscopy.

Dilute liquid crystals used to enhance residual dipolar couplings may alter conformational equilibrium in oligosaccharides

The solution structures of a trisaccharide and a pentasaccharide containing the Lewis(x) motif were determined by two independent approaches using either dipolar cross-relaxation (NOE) or residual dipolar coupling (RDC) data. For the latter, one-bond 13C[bond](1)H RDC enhanced by two different mineral liquid crystals were used alone. Home-written programs were employed firstly for measuring accurately the coupling constants in the direct dimension of non-decoupled HSQC experiments, secondly for transforming each RDC data set into geometrical restraints. In this second program, the complete molecular structure was expressed in a unique frame where the alignment tensor is diagonal. Assuming that the pyranose rings are rigid, their relative orientation is defined by optimizing the glycosidic torsion angles. For the trisaccharide, a good agreement was observed between the results of both approaches (NOE and RDC). In contrast, for the pentasaccharide, strong discrepancies appeared, which seem to result from interactions between the pentasaccharide and the mesogens, affecting conformational equilibrium. This observation is of importance, as it reveals that using simultaneously NOE and RDC can be hazardous as the former represent 99% of the molecules free in solution, whereas the latter correspond to less than 1% of the structure bound to the mesogen.

The evolution of population stability as a by-product of life-history evolution

Proposed mechanisms for the evolution of population stability include group selection through longterm persistence, individual selection acting directly on stability determining the demographic parameters, and the evolution of stability as a by-product of life-history evolution. None of these hypotheses currently has clear empirical support. Using two sets of Drosophila melanogaster populations, we provide experimental evidence of stability evolving as a correlated response to selection on traits not directly related to demography. Four populations (FEJs) were selected for faster development and early reproduction for 125 generations, and the other four (JBs) were ancestral controls. All FEJ and JB populations have been maintained on discrete generations at moderate density, thus eliminating differential selection on stability determining demographic parameters. We derived eight small populations from each FEJ and JB population, and subjected four small populations each to either stabilizing or destabilizing food regimes. Census data on these 64 small populations over 20 generations clearly showed that the FEJ populations have significantly less temporal fluctuations in their numbers in both food regimes compared to their controls. This greater stability of the FEJ populations is probably a by-product of the evolution of reduced fecundity and pre-adult survivorship, as a correlated response to selection for rapid development.

Role for NMR in structural genomics

The 2nd EMSL Workshop on Structural Genomics was held on 28th and 29th July 2000 at the Environmental Molecular Sciences Laboratory at the Department of Energy's Pacific Northwest National Laboratory in Richland, WA. The workshop focused on four topics: 1. The role for NMR in structural and functional genomics; 2. The technical challenges NMR faces for structural and functional genomics; 3. The potential need for a national NMR center for structural and functional genomics in the United States; and 4. Organization of the NMR community. This report summarizes the workshop proceedings and conclusions reached regarding the role of NMR in the emerging fields of structural and functional genomics.

Global orientation of bound MMP-3 and N-TIMP-1 in solution via residual dipolar couplings

Crystal structures of catalytic domains of MMP-3 and MT1-MMP bound to TIMP-1 or TIMP-2, respectively, differ in the orientation of the TIMP in the MMP active site. The orientation in solution of N-TIMP-1 in the MMP-3 active site has been investigated using residual dipolar couplings (RDCs). Fitting of the RDCs to the X-ray structures of the complexes suggests general agreement with the orientation of crystalline MMP-3(DeltaC) and TIMP-1 and a large disparity from the orientation of crystalline MT1-MMP(DeltaC) and TIMP-2. Rigid body docking of MMP-3 and N-TIMP-1 X-ray coordinates using RDCs and intermolecular NOEs provided a time-averaged orientation in solution differing from the crystal structure by a 5 degrees rotation toward the MT1-MMP(DeltaC)/TIMP-2 orientation. The slight discrepancy in orientations in solution and crystal lies within the experimental uncertainties. Intermolecular NOEs used in the docking corroborated the accuracy of mapping the interface by a paramagnetic NMR footprinting assay, a potential alternative source of contacts for docking. Some uncertainty in the N-TIMP-1 orientation in the MMP-3 active site, coupled with microsecond to millisecond fluctuations of the MMP-binding ridge of N-TIMP-1 in the complex and flexibility in MMP-3(DeltaC) S(1)' to S(3)' subsites, leaves open the possibility that N-TIMP-1 might dynamically pivot a few degrees or more in the arc toward the MT1-MMP(DeltaC)/TIMP-2 orientation. Differing TIMP orientations in MMP active sites are more likely to result from structural differences in TIMP AB hairpin loops than from crystal packing artifacts.