Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta

New experimental evidence for pervasive dynamics in proteins

There is ample computational, but only sparse experimental data suggesting that pico-ns motions with 1 Å amplitude are pervasive in proteins in solution. Such motions, if present in reality, must deeply affect protein function and protein entropy. Several NMR relaxation experiments have provided insights into motions of proteins in solution, but they primarily report on azimuthal angle variations of vectors of covalently-linked atoms. As such, these measurements are not sensitive to distance fluctuations, and cannot but under-represent the dynamical properties of proteins. Here we analyze a novel NMR relaxation experiment to measure amide proton transverse relaxation rates in uniformly 15 N labeled proteins, and present results for protein domain GB1 at 283 and 303 K. These relaxation rates depend on fluctuations of dipolar interactions between 1 HN and many nearby protons on both the backbone and sidechains. Importantly, they also report on fluctuations in the distances between these protons. We obtained a large mismatch between rates computed from the crystal structure of GB1 and the experimental rates. But when the relaxation rates were calculated from a 200 ns molecular dynamics trajectory using a novel program suite, we obtained a substantial improvement in the correspondence of experimental and theoretical rates. As such, this work provides novel experimental evidence of widespread motions in proteins. Since the improvements are substantial, but not sufficient, this approach may also present a new benchmark to help improve the theoretical forcefields underlying the molecular dynamics calculations.

NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins

Intrinsically disordered proteins are ubiquitous throughout all known proteomes, playing essential roles in all aspects of cellular and extracellular biochemistry. To understand their function, it is necessary to determine their structural and dynamic behavior and to describe the physical chemistry of their interaction trajectories. Nuclear magnetic resonance is perfectly adapted to this task, providing ensemble averaged structural and dynamic parameters that report on each assigned resonance in the molecule, unveiling otherwise inaccessible insight into the reaction kinetics and thermodynamics that are essential for function. In this review, we describe recent applications of NMR-based approaches to understanding the conformational energy landscape, the nature and time scales of local and long-range dynamics and how they depend on the environment, even in the cell. Finally, we illustrate the ability of NMR to uncover the mechanistic basis of functional disordered molecular assemblies that are important for human health.

Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation

Amino-acid side-chain properties in proteins are key determinants of protein function. NMR spin relaxation of side chains is an important source of information about local protein dynamics and flexibility. However, traditional solution NMR relaxation methods are most sensitive to sub-nanosecond dynamics lacking information on slower ns-μs time-scale motions. Nanoparticle-assisted NMR spin relaxation (NASR) of methyl-side chains is introduced here as a window into these ns-μs dynamics. NASR utilizes the transient and nonspecific interactions between folded proteins and slowly tumbling spherical nanoparticles (NPs), whereby the increase of the relaxation rates reflects motions on time scales from ps all the way to the overall tumbling correlation time of the NPs ranging from hundreds of ns to μs. The observed motional amplitude of each methyl group can then be expressed by a model-free NASR S² order parameter. The method is demonstrated for ²H-relaxation of CH₂D methyl moieties and cross-correlated relaxation of CH₃ groups for proteins Im7 and ubiquitin in the presence of anionic silica-nanoparticles. Both types of relaxation experiments, dominated by either quadrupolar or dipolar interactions, yield highly consistent results. Im7 shows additional dynamics on the intermediate time scales taking place in a functionally important loop, whereas ubiquitin visits the majority of its conformational substates on the sub-ns time scale. These experimental observations are in good agreement with 4-10 μs all-atom molecular dynamics trajectories. NASR probes side-chain dynamics on a much wider range of motional time scales than previously possible, thereby providing new insights into the interplay between protein structure, dynamics, and molecular interactions that govern protein function.

Simultaneous measurement of 1HC/N-R2's for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins

Paramagnetic relaxation enhancements (PREs) are routinely used to provide long-range distance restraints for the determination of protein structures, to resolve protein dynamics, ligand-protein binding sites, and lowly populated species, using Nuclear Magnetic Resonance Spectroscopy (NMR). Here, we propose a simultaneous ¹H-¹⁵ N, ¹H-¹³C SESAME based pulse scheme for the rapid acquisition of ¹H^C/N-R₂ relaxation rates for the determination of backbone and sidechain PREs of proteins. The ¹H^N-R₂ rates from the traditional and our approach on Ubiquitin (UBQ) are well correlated (R² = 0.99), revealing their potential to be used quantitatively. Comparison of the S57C UBQ calculated and experimental PREs provided backbone and side chain Q factors of 0.23 and 0.24, respectively, well-fitted to the UBQ NMR structure, showing that our approach can be used to acquire accurate PRE rates from the functionally important sites of proteins but in at least half the time as traditional methods.

Atomic resolution conformational dynamics of intrinsically disordered proteins from NMR spin relaxation

Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental approaches for investigating the conformational behaviour of intrinsically disordered proteins (IDPs). IDPs represent a significant fraction of all proteomes, and, despite their importance for understanding fundamental biological processes, the molecular basis of their activity still remains largely unknown. The functional mechanisms exploited by IDPs in their interactions with other biomolecules are defined by their intrinsic dynamic modes and associated timescales, justifying the considerable interest over recent years in the development of technologies adapted to measure and describe this behaviour. NMR spin relaxation delivers information-rich, site-specific data reporting on conformational fluctuations occurring throughout the molecule. Here we review recent progress in the use of ¹⁵N relaxation to identify local backbone dynamics and long-range chain-like motions in unfolded proteins.

An introduction to biological NMR spectroscopy

NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP).

Separability between overall and internal motion: a protein folding problem

The separability between overall and internal motions is evaluated over multiple folding trajectories of the villin headpiece subdomain. The analysis, which relies on the Prompers-Brüschweiler separability index, offers a potentially useful perspective on protein folding. The protein is considered folded in this study, not when it reaches some static target, but rather when it tumbles as a dynamically constrained object. The analysis also demonstrates how the separability index, when applied to protein folding simulations, can facilitate the analysis of NMR relaxation data.

Toward a predictive understanding of slow methyl group dynamics in proteins

The development of the most recent generation of molecular mechanics force fields promises an increasingly predictive understanding of the protein dynamics-function relationship. Based on extensive validation against various types of experimental data, the AMBER force field ff99SB was benchmarked in recent years as a favorable force field for protein simulations. Recent improvements of the side chain and backbone potentials, made by different groups, led to the ff99SB-ILDN and ff99SBnmr1 force fields, respectively. The combination of these potentials into a unified force field, termed ff99SBnmr1-ILDN, was used in this study to perform a microsecond time scale molecular dynamics simulation of free ubiquitin in explicit solvent for validation against an extensive set of experimental NMR methyl group residual dipolar couplings. Our results show a high level of consistency between the experimental data and the values predicted from the molecular dynamics trajectory reflecting a systematically improved performance of ff99SBnmr1-ILDN over the original ff99SB force field. Moreover, the unconstrained ff99SBnmr1-ILDN MD ensemble achieves a similar level of agreement as the recently introduced EROS ensemble, which was constructed based on a large body of NMR data as constraints, including the methyl residual dipolar couplings. This suggests that ff99SBnmr1-ILDN provides a high-quality representation of the motions of methyl-bearing protein side chains, which are sensitive probes of protein-protein and protein-ligand interactions.

Solution NMR spectroscopy of supra-molecular systems, why bother? A methyl-TROSY view

With the development of appropriate labeling schemes and the associated experiments that exploit them it has become possible to record high quality solution NMR spectra of supra-molecular complexes with molecular masses extending to 1MDa. One such approach involves selective (13)CH(3) methyl labeling in highly deuterated proteins using experiments that make use of a methyl-TROSY effect that significantly improves both resolution and sensitivity in spectra. The utility of this methodology has been demonstrated on a growing number of interesting particles. It seems appropriate at this juncture, therefore, to 'step back' and evaluate the role that solution NMR spectroscopy can play in what has traditionally been the domain of X-ray crystallography and more recently cryo-electron microscopy. It is argued here that solution NMR can make a critical contribution to our understanding of how dynamics regulate function in these high molecular weight systems. Several examples from work in my laboratory on the proteasome are presented as an illustration.

Measurement of methyl group motional parameters of invisible, excited protein states by NMR spectroscopy

An understanding of many biological processes can only be achieved through studies of the structure (enthalpy) and motions (entropy) of the key molecules that are involved, including those that are formed only transiently and with low population. These transiently formed, low populated states are invisible to most biophysical techniques but in many cases they can be studied in detail using relaxation dispersion NMR spectroscopy. Relaxation dispersion methodology has recently been described for the measurement of protein backbone excited state chemical shifts as well as bond vector orientations, which form the basis for structural studies of these invisible conformers. It is of interest to extend such studies by quantifying motional parameters of the excited state, providing a more complete description of the energy landscape that drives the biochemical event in question. Herein we describe a relaxation dispersion method for measuring site-specific motional parameters of methyl containing residues in the excited state. The approach is applied to the invisible unfolded state of the G48M Fyn SH3 domain that is in exchange with the folded conformation. Not surprisingly, the degree of disorder is in general higher in the unfolded state than in the folded conformer, although there is some ordering of side-chains in the unfolded state toward the C-terminal region of the domain. The development of the present methodology provides the first step toward characterizing the motional properties of invisible conformers, complementing the structural information that is already available from relaxation dispersion studies.

Biophysical study of thermal denaturation of apo-calmodulin: dynamics of native and unfolded states

Apo-calmodulin, a small, mainly alpha, soluble protein is a calcium-dependent protein activator. This article presents a study of internal dynamics of native and thermal unfolded apo-calmodulin, using quasi-elastic neutron scattering. This technique can probe protein internal dynamics in the picosecond timescale and in the nanometer length-scale. It appears that a dynamical transition is associated with thermal denaturation of apo-calmodulin. This dynamical transition goes together with a decrease of the confinement of hydrogen atoms, a decrease of immobile protons proportion and an increase of dynamical heterogeneity. The comparison of native and unfolded states dynamics suggests that the dynamics of protein atoms is more influenced by their distance to the backbone than by their solvent exposure.

Methyl dynamics of the amyloid-β peptides Aβ40 and Aβ42

To probe the role of side chain dynamics in Abeta aggregation, we studied the methyl dynamics of native Abeta40 and Abeta42 by measuring cross relaxation rates with interleaved data collection. The methyl groups in the C-terminus are in general more rigid in Abeta42 than in Abeta40, consistent with previous results from backbone (15)N dynamics. This lends support to the hypothesis that a rigid C-terminus in Abeta42 may serve as an internal aggregation seed. Interestingly, two methyl groups of V18 located in the central hydrophobic cluster are more mobile in Abeta42 than in Abeta40, most likely due to the paucity of V18 intra-molecular interactions in Abeta42. V18 may then be more available for inter-molecular interactions to form Abeta42 aggregates. Thus, the side chain mobility of the central hydrophobic cluster may play an important role in Abeta aggregation and may contribute to the difference in aggregation propensity between Abeta40 and Abeta42.

The intrinsically disordered TC-1 interacts with Chibby via regions with high helical propensity

Thyroid cancer 1 (TC-1) is a 106-residue naturally disordered protein that has been found to associate with thyroid, gastric, and breast cancers. Recent studies showed that the protein functions as a positive regulator in the Wnt/beta-catenin signaling pathway, a pathway that is known to play essential roles in developmental processes and causes tumor formation when misregulated. By competing with beta-catenin for binding to Chibby (Cby), a conserved nuclear protein that antagonizes the beta-catenin-mediated transcriptions, TC-1 up-regulates a number of beta-catenin target genes that are known to be involved in the aggressive behavior of cancers. In order to gain a molecular understanding of the role TC-1 plays in regulating the Wnt/beta-catenin signaling pathway, detailed structural studies of the protein and its interaction with Cby are essential. In this work, we used nuclear magnetic resonance (NMR) spectroscopy to elucidate the structure of TC-1 and its interaction with Cby. Our results indicate that even though TC-1 is naturally disordered, the protein adopts fairly compact conformations under nondenaturing conditions. Chemical shift analysis and relaxation measurements show that three regions (D44-R53, K58-A64, and D73-T88) with high-helical propensity are present in the C-terminal portion of TC-1. Upon addition of Cby, significant broadening of resonance signals derived from these helical regions of TC-1 was observed. The result indicates that the intrinsically disordered TC-1 interacts with Cby via its transient helical structure.

Intrinsic dynamics of the partly unstructured PX domain from the Sendai virus RNA polymerase cofactor P

Despite their evident importance for function, dynamics of intrinsically unstructured proteins are poorly understood. Sendai virus phosphoprotein, cofactor of the RNA polymerase, contains a partly unstructured protein domain. The phosphoprotein X domain (PX) is responsible for binding the polymerase to the nucleocapsid assembling the viral RNA. For RNA synthesis, the interplay of the dynamics of the unstructured and structured PX subdomains is thought to drive progression of the RNA polymerase along the nucleocapsid. Here we present a detailed study of the dynamics of PX using hydrogen/deuterium exchange and different NMR relaxation measurements. In the unstructured subdomain, large amplitude fast motions were found to be fine-tuned by the presence of residues with short side chains. In the structured subdomain, where fast motions of both backbone and side chains are fairly restricted, the first helix undergoes slow conformational exchange corresponding to a local unfolding event. The other two helices, which represent the nucleocapsid binding site, were found to be more stable and to reorient with respect to each other, as probed by slow conformational exchange identified for residues on the third helix. The study illustrates the intrinsically differential dynamics of this partly unstructured protein and proposes the relation between these dynamics and its function.

Probing nascent structures in peptides using natural abundance 13C NMR relaxation and reduced spectral density mapping

The main chain motional properties for a series of peptides that appear to have preferred conformations in solution have been systematically studied using solution-state nuclear magnetic resonance spectroscopy. The series of peptides were derived from the N-termini of pro-inflammatory chemokine proteins and HoxB1, a transcriptional regulator. As an unstructured control, a ten residue peptide was designed, synthesized, and found to be minimally structured from solution NMR data. The dynamic properties of the main chain for the peptides were assessed through longitudinal and transverse main chain (13)Calpha relaxation rates and the heteronuclear nuclear Overhauser effect. Motional parameters were interpreted using reduced spectral density mapping and compared with those derived from an extended Lipari-Szabo model in which the rotational correlation time was calculated for each main chain site of the peptide. Comparison of spectral density and Lipari-Szabo analyses for the peptides to those of the unstructured control peptide reveals significant differences in the dynamic behavior of the peptides. The amplitude of picosecond to nanosecond timescale motions for the main chain is observed to decrease for all of the chemokine peptides and HoxB1 over the regions that show partial structure at low temperatures. Comparatively, changes in picosecond to nanosecond timescale motions for the unstructured control peptide show no correlation with sequence position. These results indicate that there are distinguishable low temperature motional differences between an intrinsically unstructured peptide and peptides that have an inherent propensity to structure.

Characterisation of the Conformational Properties of Urea-unfolded Im7: Implications for the Early Stages of Protein Folding

The colicin immunity protein Im7 folds from its unfolded state in 6 M urea to its native four-helix structure through an on-pathway intermediate that lacks one of the helices of the native structure (helix III). In order to further characterize the folding mechanism of Im7, we have studied the conformational properties of the protein unfolded in 6 M urea in detail using heteronuclear NMR. Triple-resonance experiments with 13C/15N-labelled Im7 in 6 M urea provided almost complete resonance assignments for the backbone nuclei, and measurement of backbone 15N relaxation parameters allowed dynamic ordering of the unfolded polypeptide chain to be investigated. Reduced spectral density mapping and fitting backbone R2 relaxation rates to a polymer dynamics model identified four clusters of interacting residues, each predicted by the average area buried upon folding for each residue. Chemical shift analyses and measurement of NOEs detected with a long mixing-time 1H-1H-15N NOESY-HSQC spectrum confirmed the formation of four clusters. Each cluster of interacting side-chains in urea-unfolded Im7 occurs in a region of the protein that forms a helix in the protein, with the largest clusters being associated with the three long helices that are formed in the on-pathway folding intermediate, whilst the smallest cluster forms a helix only in the native state. NMR studies of a Phe15Ala Im7 variant and a protein in which residues 51-56 are replaced by three glycine residues (H3G3 Im7*), indicated that the clusters do not interact with each other, possibly because they are solvated by urea, as indicated by analysis of NOEs between the protein and the solvent. Based on these data, we suggest that dilution of the chaotrope to initiate refolding will result in collapse of the clusters, leading to the formation of persistent helical structure and the generation of the three-helix folding intermediate.

Quantitation of the nearest-neighbour effects of amino acid side-chains that restrict conformational freedom of the polypeptide chain using reversed-phase liquid chromatography of synthetic model peptides with L- and D-amino acid substitutions

Side-chain backbone interactions (or "effects") between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects (i to i+1) in peptides through reversed-phase liquid chromatography (RP-HPLC) of model synthetic peptides, where L- and D-amino acids were substituted at the N-terminal end of the peptide sequence, adjacent to a L-Leu residue. These nearest-neighbour effects (expressed as the difference in retention times of L- and D-peptide diastereomers at pHs 2 and 7) were frequently dramatic, depending on the type of side-chain adjacent to the L-Leu residue, albeit such effects were independent of mobile phase conditions. No nearest-neighbour effects were observed when residue i is adjacent to a Gly residue. Calculation of minimum energy conformations of selected peptides supported the view that, whether a L- or D-amino acid is substituted adjacent to L-Leu, its orientation relative to this bulky Leu side-chain represents the most energetically favourable configuration. We believe that such energetically favourable, and different, configurations of L- and D-peptide diastereomers affect their respective interactions with a hydrophobic stationary phase, which are thus quantified by different RP-HPLC retention times. Side-chain hydrophilicity/hydrophobicity coefficients were generated in the presence of these nearest-neighbour effects and, despite the relative difference in such coefficients generated from peptides substituted with L- or D-amino acids, the relative difference in hydrophilicity/hydrophobicity between different amino acids in the L- or D-series is maintained. Overall, our results demonstrate that such nearest-neighbour effects can clearly restrict conformational space of an amino acid side-chain in a polypeptide chain.

Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease

The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular dynamics simulations to characterise the residual structure of the Delta131Delta fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that Delta131Delta under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology.

Motional properties of unfolded ubiquitin: a model for a random coil protein

The characterization of unfolded states of proteins has recently attracted considerable interest, as the residual structure present in these states may play a crucial role in determining their folding and misfolding behavior. Here, we investigated the dynamics in the denatured state of ubiquitin in 8 M urea at pH2. Under these conditions, ubiquitin does not have any detectable local residual structure, and uniform 15N relaxation rates along the sequence indicate the absence of motional restrictions caused by residual secondary structure and/or long-range interactions. A comparison of different models to predict relaxation data in unfolded proteins suggests that the subnanosecond dynamics in unfolded states depend on segmental motions only and do not show a dependence on the residue type but for proline and glycine residues.

pH dependence of amide chemical shifts in natively disordered polypeptides detects medium-range interactions with ionizable residues

A growing number of natively disordered proteins undergo a folding/binding process that is essential for their biological function. An interesting question is whether these proteins have incompletely solvated regions that drive the folding/binding process. Although the presence of predominantly hydrophobic buried regions can be easily ascertained by high-sensitivity differential scanning calorimetry analysis, the identification of those residues implicated in the burial requires NMR analysis. We have selected a partially solvated natively disordered fragment of Escherichia coli, thioredoxin, C37 (38-108), for full NMR spectral assignment. The secondary chemical shifts, temperature coefficients, and relaxation rates (R(1) and R(2)) of this fragment indicate the presence of a flexible backbone without a stable hydrogen bond network near neutral pH. (1)H-(15)N heteronuclear single quantum coherence analysis of the pH dependence of amide chemical shifts in fragment C37 within pH 2.0 and 7.0 suggests the presence of interactions between nonionizable residues and the carboxylate groups of four Asp and four Glu residues. The pH midpoints (pH(m)) of the amides in the ionizable residues (Asp or Glu) and, consequently, the shifts in the pH(m) (DeltapH(m)) of these residues with respect to model tetrapeptides, are sequence-dependent; and the nonionizable residues that show pH dependence cluster around the ionizable ones. The same pH dependence has been observed in two fragments: M37 (38-73) and C73 (74-108), ruling out the participation of long-range interactions. Our studies indicate the presence of a 15-residue pH-dependent segment with the highest density of ionizable sites in the disordered ensembles of fragments C37 and M37. The observed correlations between ionizable and nonionizable residues in this segment suggest the organization of the backbone and side chains through local and medium-range interactions up to nine residues apart, in contrast to only a few interactions in fragment C73. These results agree qualitatively with the predominantly hydrophobic buried surface detected only in fragments C37 and M37 by highly sensitive differential scanning calorimetry analysis. This work offers a sensitive and rapid new tool to obtain clues about local and nonlocal interactions between ionizable and nonionizable residues in the growing family of natively disordered small proteins with full NMR assignments.

What Contributions to Protein Side-chain Dynamics are Probed by NMR Experiments? A Molecular Dynamics Simulation Analysis

Molecular dynamics simulations of the structurally homologous proteins TNfn3 and FNfn10 have been used to investigate the contributions to side-chain dynamics measured by NMR relaxation experiments. The results reproduce the variation in core side-chain dynamics observed by NMR and highlight the relevance of anharmonic motion and transitions between local minima for explaining NMR side-chain order parameters. A method is described for calculating converged order parameters by use of replica exchange molecular dynamics in conjunction with an implicit solvent model. These simulations allow the influence of various factors, such as the flexibility of side-chains and their free volume, on the mobility to be tested by perturbing the system. Deletion mutations are found to have the largest effect on the more densely packed FNfn10. Some counterintuitive effects are seen, such as an increase in order parameters close to deletion mutation sites, but these can be rationalized in terms of direct interactions with the modified side-chains. A statistical analysis of published order parameters supports the conclusions drawn from the simulations.

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.

Combining prediction, computation and experiment for the characterization of protein disorder

Several computational and experimental methods exist for identifying disordered residues within proteins. Computational algorithms can now identify these disordered sequences and predict their occurrence within genomes with relatively high accuracy. Recent advances in NMR and mass spectroscopy permit faster and more detailed studies of disordered states at atomic resolutions. Combining prediction, computation and experimentation is proposed to accelerate and enhance the characterization of intrinsically disordered protein.

Towards complete descriptions of the free-energy landscapes of proteins

In recent years increasingly detailed information about the structures and dynamics of protein molecules has been obtained by innovative applications of experimental techniques, in particular nuclear magnetic resonance spectroscopy and protein engineering, and theoretical methods, notably molecular dynamics simulations. In this article we discuss how such approaches can be combined by incorporating a wide range of different types of experimental data as restraints in computer simulations to provide unprecedented detail about the ensembles of structures that describe proteins in a wide variety of states from the native structure to highly unfolded species. Knowledge of these ensembles is beginning to enable the complete free-energy landscapes of individual proteins to be defined at atomic resolution. This strategy has provided new insights into the mechanism by which proteins are able to fold into their native states, or by which they fail to do so and give rise to harmful aggregates that are associated with a wide range of debilitating human diseases.

Elucidation of the Protein Folding Landscape by NMR

NMR is one of the few experimental methods that can provide detailed insights into the structure and dynamics of unfolded and partly folded states of proteins. Mapping the protein folding landscape is of central importance to understanding the mechanism of protein folding. In addition, it is now recognized that many proteins are intrinsically unstructured in their functional states, while partly folded states of several cellular proteins have been implicated in amyloid disease. NMR is uniquely suited to characterize the structures present in the conformational ensemble and probe the dynamics of the polypeptide chain in unfolded and partially folded protein states.

Stabilizing and Destabilizing Clusters in the Hydrophobic Core of Long Two-stranded α-Helical Coiled-coils

Detailed sequence analyses of the hydrophobic core residues of two long two-stranded alpha-helical coiled-coils that differ dramatically in sequence, function, and length were performed (tropomyosin of 284 residues and the coiled-coil domain of the myosin rod of 1086 residues). Three types of regions were present in the hydrophobic core of both proteins: stabilizing clusters and destabilizing clusters, defined as three or more consecutive core residues of either stabilizing (Leu, Ile, Val, Met, Phe, and Tyr) or destabilizing (Gly, Ala, Cys, Ser, Thr, Asn, Gln, Asp, Glu, His, Arg, Lys, and Trp) residues, and intervening regions that consist of both stabilizing and destabilizing residues in the hydrophobic core but no clusters. Subsequently, we designed a series of two-stranded coiled-coils to determine what defines a destabilizing cluster and varied the length of the destabilizing cluster from 3 to 7 residues to determine the length effect of the destabilizing cluster on protein stability. The results showed a dramatic destabilization, caused by a single Leu to Ala substitution, on formation of a 3-residue destabilizing cluster (DeltaT(m) of 17-21 degrees C) regardless of the stability of the coiled-coil. Any further substitution of Leu to Ala that increased the size of the destabilizing cluster to 5 or 7 hydrophobic core residues in length had little effect on stability (DeltaT(m) of 1.4-2.8 degrees C). These results suggested that the contribution of Leu to protein stability is context-dependent on whether the hydrophobe is in a stabilizing cluster or its proximity to neighboring destabilizing and stabilizing clusters.