Diffusion NMR spectroscopy: folding and aggregation of domains in p53

Water diffusion in complex systems measured by PGSE NMR using chemical shift selective stimulated echo: Elimination of magnetization exchange effects

The interpretation of molecular translational diffusion as measured by pulsed gradient spin-echo NMR (PGSE NMR) can be complicated by the presence of chemical exchange and/or dipolar cross-relaxation (including relayed cross-relaxation via spin diffusion). The magnitude of influence depends on the kinetics of exchange and/or dipolar cross-relaxation present within the system as well as the PGSE NMR sequences chosen for measurements. First, we present an exchange induced zero-crossing phenomenon for signal attenuation of water in lipidic cubic phases (formed by a mixture of monoolein and water) in the presence of pulsed gradients observed using a standard STimulated Echo (STE) sequence. This magnetization exchange induced zero-crossing phenomenon, a pseudo-negative diffraction-like feature, resembles that reported previously for restricted diffusion when locally anisotropic pores are polydisperse or randomly oriented. We then demonstrate the elimination of these exchange and/or dipolar cross-relaxation induced effects with the use of a chemical shift selective STE (CHESS-STE) sequence, adapted from the previously reported band-selective short transient STE sequence, along with results obtained from the bipolar pulse pair STE sequence for comparison. The CHESS-STE sequence introduced here represents a generic form of PGSE NMR sequences for obtaining water diffusion coefficients free from the influence of exchange and/or dipolar cross-relaxation in complex systems. It has potential applications in measuring translational diffusion of water in biopolymer mixtures as well as probing the microscopic structure in materials via water restricted diffusion measured by PGSE NMR, particularly when the potential presence of exchange/cross-relaxation is of concern.

Size Determination of Protein Oligomers/Aggregates Using Diffusion NMR Spectroscopy

Diffusion-ordered spectroscopy (DOSY) is a widely used NMR technique for the identification of different chemical moieties/compounds contained in mixtures and has been successfully employed for the separation of small molecules based on hydrodynamic radii. Herein we show that DOSY can also be applied for the size determination of larger biomolecules such as proteins and protein oligomers/aggregates. Proof-of-principle is first shown with a cross-linked oligomeric protein mixture where the hydrodynamic volumes of each component are estimated and subsequently verified with size-exclusion HPLC and SDS polyacrylamide gel electrophoresis. We then determine the sizes of protein oligomers contained in a protein solution subjected under amyloid fibrillogenesis conditions. These studies aim to provide insight into the kinetics behind protein aggregation involved in amyloidosis as well as to determine the hydrodynamic radii of proteins within the mixture.

Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins

The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.

Translational diffusion of unfolded and intrinsically disordered proteins

Translational (or self-diffusion) coefficient in dilute solution is inversely proportional to the size of a diffusing molecule, and hence self-diffusion coefficient measurements have been applied to determine the effective hydrodynamic radii for a range of native and nonnative protein conformations. In particular, translational diffusion coefficient measurements are useful to estimate the hydrodynamic radius of natively (or intrinsically) disordered proteins in solution, and, thereby, probe the compactness of a protein as well as its change when environmental parameters such as temperature, solution pH, or protein concentration are varied. The situation becomes more complicated in concentrated solutions. In this review, we discuss the translational diffusion of disordered proteins in dilute and crowded solutions, focusing primarily on the information provided by pulsed-field gradient NMR technique, and draw analogies to well-structured globular proteins and synthetic polymers.

Diffusion Profiling of Therapeutic Proteins by Using Solution NMR Spectroscopy

Characterizing changes to structure and behavior is an important aspect of therapeutic protein development. NMR spectroscopy is well suited to study interactions and higher-order structure that could impact biological function and safety. We used NMR diffusion methods to describe the overall behavior of proteins in solution by defining a "diffusion profile" that captures the complexities in diffusion behavior. Diffusion profiles offer a simple means to interpret protein solution behavior as a distribution of sizes and association states. As a characterization method, diffusion profiling is well suited to complement and augment traditional biophysical and NMR methods to probe the solution behavior of therapeutic proteins.

Measuring translational diffusion of 15N-enriched biomolecules in complex solutions with a simplified 1H-15N HMQC-filtered BEST sequence

Pulsed-field gradient nuclear magnetic resonance has seen an increase in applications spanning a broad range of disciplines where molecular translational diffusion properties are of interest. The current study introduces and experimentally evaluates the measurement of translational diffusion coefficients of ¹⁵N-enriched biomolecules using a ¹H-¹⁵N HMQC-filtered band-selective excitation short transient (BEST) sequence as an alternative to the previously described SOFAST-XSTE sequence. The results demonstrate that accurate translational diffusion coefficients of ¹⁵N-labelled peptides and proteins can be obtained using this alternative ¹H-¹⁵N HMQC-filtered BEST sequence which is implementable on NMR spectrometers equipped with probes fitted with a single-axis field gradient, including most cryoprobes dedicated to bio-NMR. The sequence is of potential use for direct quantification of protein or peptide translational diffusion within complex systems, such as in mixtures of macromolecules, crowded solutions, membrane-mimicking media and in bicontinuous cubic phases, where conventional sequences may not be readily applicable due to the presence of intense signals arising from sources other than the protein or peptide under investigation.

An enhanced sensitivity methyl 1H triple-quantum pulse scheme for measuring diffusion constants of macromolecules

We present a pulse scheme that exploits methyl ¹H triple-quantum (TQ) coherences for the measurement of diffusion rates of slowly diffusing molecules in solution. It is based on the well-known stimulated echo experiment, with encoding and decoding of TQ coherences. The size of quantifiable diffusion coefficients is thus lowered by an order of magnitude with respect to single-quantum (SQ) approaches. Notably, the sensitivity of the scheme is high, approximately ¾ that of the corresponding single quantum experiment, neglecting relaxation losses, and on the order of a factor of 4 more sensitive than a previously published sequence for AX₃ spin systems (Zheng et al. in JMR 198:271-274, 2009) for molecules that are only ¹³C labeled at the methyl carbon position. Diffusion coefficients measured from TQ- and SQ-based experiments recorded on a range of protein samples are in excellent agreement. We present an application of this technique to the study of phase-separated proteins where protein concentrations in the condensed phase can exceed 400 mg/mL, diffusion coefficients can be as low as ~10^-9 cm²s^-1 and traditional SQ experiments fail.

Effect of Intrinsic Disorder and Self-Association on the Translational Diffusion of Proteins: The Case of α-Casein

Translational diffusion is the major mode of macromolecular transport in leaving organisms, and therefore it is vital to many biological and biotechnological processes. Although translational diffusion of proteins has received considerable theoretical and experimental scrutiny, much of that attention has been directed toward the description of globular proteins. The translational diffusion of intrinsically disordered proteins (IDPs), however, is much less studied. Here, we use a pulsed-gradient nuclear magnetic resonance technique (PFG NMR) to investigate the translational diffusion of a disordered protein in a wide range of concentrations using α-casein that belongs to the class of natively disordered proteins as an example.

Pulsed-field gradient nuclear magnetic resonance measurements (PFG NMR) for diffusion ordered spectroscopy (DOSY) mapping

The advent of Diffusion Ordered SpectroscopY (DOSY) NMR has enabled diffusion coefficients to be routinely measured and used to characterize chemical systems in solution. Indeed, DOSY NMR allows the separation of the chemical entities present in multicomponent systems and provides information on their intermolecular interactions as well as on their size and shape.

Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition

Translational diffusion is the most fundamental form of transport in chemical and biological systems. The diffusion coefficient is highly sensitive to changes in the size of the diffusing species; hence, it provides important information on the variety of macromolecular processes, such as self-assembly or folding-unfolding. Here, we investigate the behavior of the diffusion coefficient of a macromolecule in the vicinity of heat-induced transition from folded to unfolded state. We derive the equation that describes the diffusion coefficient of the macromolecule in the vicinity of the transition and use it to fit the experimental data from pulsed-field-gradient nuclear magnetic resonance (PFG NMR) experiments acquired for two globular proteins, lysozyme and RNase A, undergoing temperature-induced unfolding. A very good qualitative agreement between the theoretically derived diffusion coefficient and experimental data is observed.

Improving accuracy in DOSY and diffusion measurements using triaxial field gradients

NMR measurements of diffusion in solution, whether primarily quantitative, or, (as in DOSY, Diffusion-Ordered Spectroscopy) qualitative, can be particularly demanding. Here we show how the use of appropriate transverse (x, y) pulsed field gradients, orthogonal to the more usual z axis pulsed field gradient applied along the long axis of the sample, can greatly reduce two important sources of systematic error in diffusion experiments. These are the extra signal attenuation caused by sample convection, and gradient-dependent signal phase shifts caused by the magnetic field and field-frequency lock disturbances generated by field gradient pulses.

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy

Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D ¹H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins.

Phase separation in biology; functional organization of a higher order

Inside eukaryotic cells, macromolecules are partitioned into membrane-bounded compartments and, within these, some are further organized into non-membrane-bounded structures termed membrane-less organelles. The latter structures are comprised of heterogeneous mixtures of proteins and nucleic acids and assemble through a phase separation phenomenon similar to polymer condensation. Membrane-less organelles are dynamic structures maintained through multivalent interactions that mediate diverse biological processes, many involved in RNA metabolism. They rapidly exchange components with the cellular milieu and their properties are readily altered in response to environmental cues, often implicating membrane-less organelles in responses to stress signaling. In this review, we discuss: (1) the functional roles of membrane-less organelles, (2) unifying structural and mechanistic principles that underlie their assembly and disassembly, and (3) established and emerging methods used in structural investigations of membrane-less organelles.

Investigating the mechanisms of amylolysis of starch granules by solution-state NMR

Starch is a prominent component of the human diet and is hydrolyzed by α-amylase post-ingestion. Probing the mechanism of this process has proven challenging, due to the intrinsic heterogeneity of individual starch granules. By means of solution-state NMR, we demonstrate that flexible polysaccharide chains protruding from the solvent-exposed surfaces of waxy rice starch granules are highly mobile and that during hydrothermal treatment, when the granules swell, the number of flexible residues on the exposed surfaces increases by a factor of 15. Moreover, we show that these flexible chains are the primary substrates for α-amylase, being cleaved in the initial stages of hydrolysis. These findings allow us to conclude that the quantity of flexible α-glucan chains protruding from the granule surface will greatly influence the rate of energy acquisition from digestion of starch.

The folding of the specific DNA recognition subdomain of the sleeping beauty transposase is temperature-dependent and is required for its binding to the transposon DNA

The reaction of DNA transposition begins when the transposase enzyme binds to the transposon DNA. Sleeping Beauty is a member of the mariner family of DNA transposons. Although it is an important tool in genetic applications and has been adapted for human gene therapy, its molecular mechanism remains obscure. Here, we show that only the folded conformation of the specific DNA recognition subdomain of the Sleeping Beauty transposase, the PAI subdomain, binds to the transposon DNA. Furthermore, we show that the PAI subdomain is well folded at low temperatures, but the presence of unfolded conformation gradually increases at temperatures above 15°C, suggesting that the choice of temperature may be important for the optimal transposase activity. Overall, the results provide a molecular-level insight into the DNA recognition by the Sleeping Beauty transposase.

NMR spectroscopy and X-ray characterisation of cationic N-heteroaryl-pyridylamido Zr(IV) complexes: a further level of complexity for the elusive active species of pyridylamido olefin polymerisation catalysts

New [(N(-),N,N(-))ZrR2] dialkyl complexes (N(-),N,N(-)=pyrrolyl-pyridyl-amido or indolyl-pyridyl-amido; R=Me or CH2Ph) have been synthesised and tested as pre-catalysts for ethene and propene polymerisation in combination with different activators, such as B(C6F5)3, [Ph3C][B(C6F5)4], [HNMe2Ph][B(C6F5)4] or solid AlMe3-depleted methylaluminoxane (DMAO). Polyethylene (M(w)>2 MDa and M(w)/M(n)= 1.3-1.6) has been produced if pre-catalysts were activated with 1000 equivalents of DMAO (based on Al) [activity >1000 kg(PE)(mol([Zr]) h mol atm)(-1)] or by using a higher pre-catalyst concentration and a mixture of [HNPhMe2][B(C6F5)4] (1 equiv) and AliBu2H (60 equiv). In the case of propene polymerisation, activity has been observed only if pre-catalysts were treated with an excess of AliBu2H prior to addition of DMAO, which led to highly isotactic polypropylene ([mmmm]>95%). Neutral pre-catalysts and ion pairs derived from their activation have been characterised in solution by using advanced 1D and 2D NMR spectroscopy experiments. The detection and rationalisation of intercationic NOEs clearly showed the formation of dimeric species in which some pyrrolyl or indolyl π-electron density of one unit is engaged in stabilising the metal centre of the other unit, which relegates the counterions in the second coordination sphere. The solid-state structure of the dimeric indolyl-pyridyl-amidomethylzirconium derivative, determined by X-ray diffraction studies, points toward a weak Zr···η(3)-indolyl interaction. It can be hypothesised that the formation of dimeric cationic species hampers monomer coordination (especially of less reactive α-olefins) and that addition of AliBu2H is crucial to split the homodimers.

Proteins behaving badly: emerging technologies in profiling biopharmaceutical aggregation

Over recent decades biotechnology has made significant advances owing to the emergence of powerful biochemical and biophysical instrumentation. The development of such technologies has enabled high-throughput assessment of compounds, the implementation of recombinant DNA technology, and large-scale manufacture of monoclonal antibodies. Such innovations have ultimately resulted in the current experienced biopharmaceutical stronghold in the therapeutic market. Yet aggregate prediction and profiling remains a challenge in the formulation of biopharmaceuticals due to artifacts associated with each analytical method. We review some emerging trends and novel technologies that offer a promising potential for accurately predicting and profiling protein aggregation at various stages of biopharmaceutical product design.

Assessment of higher order structure comparability in therapeutic proteins using nuclear magnetic resonance spectroscopy

In this work, we applied nuclear magnetic resonance (NMR) spectroscopy to rapidly assess higher order structure (HOS) comparability in protein samples. Using a variation of the NMR fingerprinting approach described by Panjwani et al. [2010. J Pharm Sci 99(8):3334-3342], three nonglycosylated proteins spanning a molecular weight range of 6.5-67 kDa were analyzed. A simple statistical method termed easy comparability of HOS by NMR (ECHOS-NMR) was developed. In this method, HOS similarity between two samples is measured via the correlation coefficient derived from linear regression analysis of binned NMR spectra. Applications of this method include HOS comparability assessment during new product development, manufacturing process changes, supplier changes, next-generation products, and the development of biosimilars to name just a few. We foresee ECHOS-NMR becoming a routine technique applied to comparability exercises used to complement data from other analytical techniques.

Application of (1)H DOSY for Facile Measurement of Polymer Molecular Weights

To address the practical issues of polymer molecular weight determination, the first accurate polymer weight-average molecular weight determination method in diverse living/controlled polymerization via DOSY (diffusion-ordered NMR spectroscopy) is reported. Based on the linear correlation between the logarithm of diffusion coefficient (log D) and the molecular weights (log Mw), external calibration curves were created to give predictions of molecular weights of narrowly-dispersed polymers. This method was successfully applied to atom transfer radical polymerization (ATRP), reversible addition-fragmentation chain transfer (RAFT), and ring-opening metathesis polymerization (ROMP), with weight-average molecular weights given by this method closely correlated to those obtained from GPC measurement.

Application of diffusion-edited NMR spectroscopy for selective suppression of water signal in the determination of monomer composition in alginates

Alginate is a linear copolymer of 1-4 linked β-D-mannuronic acid (M) and 1-4 linked α-L-guluronic acid (G). The physical properties of these polysaccharides such as gel properties and viscosity are largely correlated to the monomer composition (M/G ratio), the sequence of the polymer and the molecular weight. Determination of the M/G ratio is therefore important and NMR spectroscopy is among the most common methods used to accurately obtain this ratio. Instead of using time consuming, possibly sample altering, acid hydrolysis to reduce the viscosity of the alginate sample prior to analysis, samples of low concentrations can be used. However, this results in a water peak in the NMR spectrum that is several orders of magnitude larger than the alginate signals and water suppression is required. In this article, a diffusion-edited NMR experiment that suppresses the water peak while retaining the signals of interest has been used to enable correct M/G ratio determination. This approach exploits the difference in translational diffusion between the larger alginate molecules and the smaller water molecules. Using this method, the monomer composition of 20 different alginate powders was determined. The diffusion parameters were optimized to allow measurement for samples covering a large range of M/G ratios and viscosities. Thus, such method should be useful for analyzing large numbers of unknown alginate samples using, for example, automation procedures.

Solution-state nuclear magnetic resonance spectroscopy and protein folding

A protein undergoes a variety of structural changes during its folding and misfolding and a knowledge of its behaviour is key to understanding the molecular details of these events. Solution-state NMR spectroscopy is unique in that it can provide both structural and dynamical information at both high-resolution and at a residue-specific level, and is particularly useful in the study of dynamic systems. In this chapter, we describe NMR strategies and how they are applied in the study of protein folding and misfolding.

Direct observation of minimum-sized amyloid fibrils using solution NMR spectroscopy

It is challenging to investigate the structure and dynamics of amyloid fibrils at the residue and atomic resolution because of their high molecular weight and heterogeneous properties. Here, we used solution nuclear magnetic resonance (NMR) spectroscopy to characterize the conformation and flexibility of amyloid fibrils of β2-microglobulin (β2m), for which direct observation of solution NMR could not be made. Ultrasonication led to fragmentation producing a solution of minimum-sized fibrils with a molecular weight of around 6 MDa. In 1H-15N heteronuclear single-quantum correlation measurements, five signals, derived from N-terminal residues (i.e., Ile1, Gln2, Arg3, Thr4, and Lys6), were newly detected. Signal strength decreased with the distance from the N-terminal end. Capping experiments with the unlabeled β2m monomer indicated that the signals originated from molecules located inside the fibrils. Ultrasonication makes the residues with moderate flexibility observable by reducing size of the fibrils. Thus, solution NMR measurements of ultrasonicated fibrils will be promising for studying the structure and dynamics of fibrils.

3D DOSY-TROSY to determine the translational diffusion coefficient of large protein complexes

The translational diffusion coefficient is a sensitive parameter to probe conformational changes in proteins and protein-protein interactions. Pulsed-field gradient NMR spectroscopy allows one to measure the translational diffusion with high accuracy. Two-dimensional (2D) heteronuclear NMR spectroscopy combined with diffusion-ordered spectroscopy (DOSY) provides improved resolution and therefore selectivity when compared with a conventional 1D readout. Here, we show that a combination of selective isotope labelling, 2D ¹H-¹³C methyl-TROSY (transverse relaxation-optimised spectroscopy) and DOSY allows one to study diffusion properties of large protein complexes. We propose that a 3D DOSY-heteronuclear multiple quantum coherence (HMQC) pulse sequence, that uses the TROSY effect of the HMQC sequence for ¹³C methyl-labelled proteins, is highly suitable for measuring the diffusion coefficient of large proteins. We used the 20 kDa co-chaperone p23 as model system to test this 3D DOSY-TROSY technique under various conditions. We determined the diffusion coefficient of p23 in viscous solutions, mimicking large complexes of up to 200 kDa. We found the experimental data to be in excellent agreement with theoretical predictions. To demonstrate the use for complex formation, we applied this technique to record the formation of a complex of p23 with the molecular chaperone Hsp90, which is around 200 kDa. We anticipate that 3D DOSY-TROSY will be a useful tool to study conformational changes in large protein complexes.

Characterization of the chemokine CXCL11-heparin interaction suggests two different affinities for glycosaminoglycans

Chemokines orchestrate the migration of leukocytes in the context of homeostasis and inflammation. In addition to interactions of chemokines with receptors on migrating cells, these processes require interactions of chemokines with glycosaminoglycans (GAGs) for cell surface localization. Most chemokines are basic proteins with Arg/Lys/His residue clusters functioning as recognition epitopes for GAGs. In this study we characterized the GAG-binding epitopes of the chemokine I-TAC/CXCL11. Four separate clusters of basic residues were mutated to alanine and tested for their ability to bind to GAGs in vitro and to activate the receptor, CXCR3. Mutation of a set of basic residues in the C-terminal helix (the 50s cluster, (57)KSKQAR(62)) along with Lys(17), significantly impaired heparin binding in vitro, identifying these residues as components of the dominant epitope. However, this GAG mutant retained nearly wild type receptor binding affinity, and its ability to induce cell migration in vitro was only mildly perturbed. Nevertheless, the mutant was unable to induce cell migration in vivo, establishing a requirement of CXCL11 for GAG binding for in vivo function. These studies also led to some interesting findings. First, CXCL11 exhibits conformational heterogeneity, as evidenced by the doubling of peaks in its HSQC spectra. Second, it exhibits more than one affinity state for both heparin and CXCR3, which may be related to its structural plasticity. Finally, although the binding affinities of chemokines for GAGs are typically weaker than interactions with receptors, the high affinity GAG binding state of CXCL11 is comparable with typical receptor binding affinities, suggesting some unique properties of this chemokine.

Observation of restricted diffusion in the presence of a free diffusion compartment: single- and double-PFG experiments

Theoretical and experimental studies of restricted diffusion have been conducted for decades using single pulsed field gradient (s-PFG) diffusion experiments. In homogenous samples, the diffusion-diffraction phenomenon arising from a single population of diffusing species has been observed experimentally and predicted theoretically. In this study, we introduce a composite bi-compartmental model which superposes restricted diffusion in microcapillaries with free diffusion in an unconfined compartment, leading to fast and slow diffusing components in the NMR signal decay. Although simplified (no exchange), the superposed diffusion modes in this model may exhibit features seen in more complex porous materials and biological tissues. We find that at low q-values the freely diffusing component masks the restricted diffusion component, and that prolongation of the diffusion time shifts the transition from free to restricted profiles to lower q-values. The effect of increasing the volume fraction of freely diffusing water was also studied; we find that the transition in the signal decay from the free mode to the restricted mode occurs at higher q-values when the volume fraction of the freely diffusing water is increased. These findings were then applied to a phantom consisting of crossing fibers, which demonstrated the same qualitative trends in the signal decay. The angular d-PGSE experiment, which has been recently shown to be able to measure small compartmental dimensions even at low q-values, revealed that microscopic anisotropy is lost at low q-values where the fast diffusing component is prominent. Our findings may be of importance in studying realistic systems which exhibit compartmentation.

Macrocyclic design strategies for small, stable parallel beta-sheet scaffolds

Pairs of short peptide strands can be induced to adopt an antiparallel beta-sheet secondary structure in aqueous solution via a macrocyclic constraint, as illustrated by many natural and designed peptides. We show that an analogous strategy is successful for creation of small units of parallel beta-sheet secondary structure in aqueous solution. Cyclization in this case requires nonpeptide segments for N-to-N and C-to-C interstrand linkage. Surprisingly, we find that only one of these segments needs to be preorganized.

Perspectives on NMR in drug discovery: a technique comes of age

In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility.

The effect of experimental parameters on the signal decay in double-PGSE experiments: negative diffractions and enhancement of structural information

Double pulsed gradient spin echo (d-PGSE) experiment has been recently suggested for detecting microscopic anisotropy in macroscopically isotropic samples. This sequence is complex and has many variables, including, intra alia, combinations of directions and amplitudes of the pulsed gradients, diffusion times in each of the encoding periods and the mixing time period. The effect of these experimental parameters of the d-PGSE sequence was studied in an array of water filled microcapillaries of micron diameters. We found that negative diffractions occur, as indeed predicted by recently published simulations. We also found differential effects of prolongation of the mixing time between collinear and orthogonal d-PGSE experiments. The d-PGSE experiment in the collinear direction perpendicular to the long axis of the cylinder exhibited a marked dependence on the mixing time, while the orthogonal d-PGSE experiment exhibited no such dependence at all. Interestingly, one of the most important predictions by the simulations was that the d-PGSE sequence could potentially discriminate between compartments of different sizes better than the single PGSE (s-PGSE) and it seems that our experimental results indeed corroborate these predictions.

Diacid linkers that promote parallel beta-sheet secondary structure in water

We report the development of diacid units that promote formation of a two-stranded parallel beta-sheet secondary structure between peptide segments attached via their N-termini. These linker units are formed by attaching glycine to one carboxyl group of cis-1,2-cyclohexanedicarboxylic acid (CHDA). Parallel sheet formation in water is observed when l-residue strands are attached to the CHDA-Gly unit with either of the two absolute configurations.

Analysis of an asymmetric addition with a 2:1 mixed lithium amide/n-butyllithium aggregate

A 2:1 lithium amide/ n-butyllithium aggregate 1 is investigated as an asymmetric addition template in hydrocarbon solvents. Several different chiral lithium amides were synthesized from l-valine and tested in the asymmetric addition of n-BuLi to various aldehydes. Enantiomeric excesses up to 83% were obtained in the case of the addition of n-BuLi to pivaldehyde at -116 degrees C in pentane. (1)H and (13)C INEPT DOSY were utilized to characterize a new trimeric complex 12 between 2 equiv of lithium amide and 1 equiv of lithium alkoxide. This mixed aggregate strongly indicates the possibility of product-induced chirality inhibition that is detrimental to the enantioselectivity of asymmetric addition reaction.

Contribution of rotational diffusion to pulsed field gradient diffusion measurements

NMR diffusion experiments employing pulsed field gradients are well established as sensitive probes of the displacement of individual nuclear spins in a sample. Conventionally such measurements are used as a measure of translational diffusion, but here we demonstrate that under certain conditions rotational motion will contribute very significantly to the experimental data. This situation occurs when at least one spatial dimension of the species under study exceeds the root mean square displacement associated with translational diffusion, and leads to anomalously large apparent diffusion coefficients when conventional analytical procedures are employed. We show that in such a situation the effective diffusion coefficient is a function of the duration of the diffusion delay used, and that this dependence provides a means of characterizing the dimensions of the species under investigation.

Determining accurate molecular sizes in solution through NMR diffusion spectroscopy

This tutorial review deals with the methodological procedures that can be used to obtain accurate molecular sizes in solution from diffusion NMR spectroscopy. The critical aspects associated with the estimation of the size of molecules from the measured translational self-diffusion coefficient, using the Stokes-Einstein equation, are highlighted and discussed. From a theoretical point of view, it is shown how to take into account the size of the solute with respect to that of the solvent and its non-spherical shape using the appropriate correction factors in the frictional coefficient. From a practical point of view, the advantages of introducing an internal standard in the sample are presented. Initially, non-aggregating systems are considered in an attempt to clarify what hydrodynamic dimensions mean. Successively, aggregating systems are addressed showing how it is possible to understand the aggregation level and derive the thermodynamic parameters for some illustrative aggregation processes.

Human p53 is inhibited by glutathionylation of cysteines present in the proximal DNA-binding domain during oxidative stress

The cellular mechanisms that modulate the redox state of p53 tumor suppressor remain unclear, although its DNA binding function is known to be strongly inhibited by oxidative and nitrosative stresses. We show that human p53 is subjected to a new and reversible posttranslational modification, namely, S-glutathionylation in stressed states, including DNA damage. First, a rapid and direct incorporation of biotinylated GSH or GSSG into the purified recombinant p53 protein was observed. The modified p53 had a significantly weakened ability to bind its consensus DNA sequence. Reciprocal immunoprecipitations and a GST overlay assay showed that p53 in tumor cells was marginally glutathionylated; however, the level of modification increased greatly after oxidant and DNA-damaging treatments. GSH modification coexisted with the serine phophorylations in activated p53, and the thiol-conjugated protein was present in nuclei. When tumor cells treated with camptothecin or cisplatin were subsequently exposed to glutathione-enhancing agents, p53 underwent dethiolation accompanied by detectable increases in the level of p21waf1 expression, relative to the DNA-damaging drugs alone. Mass spectrometry of GSH-modified p53 protein identified cysteines 124, 141, and 182, all present in the proximal DNA-binding domain, as the sites of glutathionylation. Biotinylated maleimide also reacted rapidly with Cys141, implying that this is the most reactive cysteine on the p53 surface. The glutathionylatable cysteines were found to exist in a negatively charged microenvironment in cellular p53. Molecular modeling studies located Cys124 and -141 at the dimer interface of p53 and showed glutathionylation of either residue would inhibit p53-DNA association and also interfere with protein dimerization. These results show for the first time that shielding of reactive cysteines contributes to a negative regulation for human p53 and imply that such an inactivation of the transcription factor may represent an acute defensive response with significant consequences for oncogenesis.

Characterisation of amyloid fibril formation by small heat-shock chaperone proteins human alphaA-, alphaB- and R120G alphaB-crystallins

AlphaB-Crystallin is a ubiquitous small heat-shock protein (sHsp) renowned for its chaperone ability to prevent target protein aggregation. It is stress-inducible and its up-regulation is associated with a number of disorders, including those linked to the deposition of misfolded proteins, such as Alzheimer's and Parkinson's diseases. We have characterised the formation of amyloid fibrils by human alphaB-crystallin in detail, and also that of alphaA-crystallin and the disease-related mutant R120G alphaB-crystallin. We find that the last 12 amino acid residues of the C-terminal region of alphaB-crystallin are predicted from their physico-chemical properties to have a very low propensity to aggregate. (1)H NMR spectroscopy reveals that this hydrophilic C-terminal region is flexible both in its solution state and in amyloid fibrils, where it protrudes from the fibrillar core. We demonstrate, in addition, that the equilibrium between different protofilament assemblies can be manipulated and controlled in vitro to select for particular alphaB-crystallin amyloid morphologies. Overall, this study suggests that there could be a fine balance in vivo between the native functional sHsp state and the formation of amyloid fibrils.