Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding

Diffusion of Peptides and Small Molecules Encapsulated in Lipidic Cubic Phases by Band-Selective Excitation Short Transient 1H PGSE NMR

In model membrane systems, such as lipidic cubic phases (LCPs), 1H NMR spectra are dominated by resonances from water and lipid molecules. The measurement of translational diffusion of peptides/molecules encapsulated in LCPs using conventional 1H pulsed-gradient spin-echo (PGSE) NMR is, therefore, immensely difficult due to the dynamic range caused by the intense resonance(s) from the surrounding environment. The present study reports the use of a band-selective short transient PGSE sequence, avoiding the perturbation of both hydration water and lipids, for measuring the diffusion of molecules encapsulated within the lipid bilayer and the aqueous channels of LCPs.

Biophysical Investigation of the Interplay between the Conformational Species of Domain-Swapped GB1 Amyloid Mutant through Real-Time Monitoring of Amyloid Fibrillation

Mutant polypeptide GB1HS#124^F26A, which is known to aggregate into amyloid-like fibrils, has been utilized as a model in this study for gaining insights into the mechanism of domain-swapped aggregation through real-time monitoring. Size exclusion with UV monitoring at 280 nm and dynamic light scattering (DLS) profiles through different time points of fibrillation reveal that the dimer transitions into monomeric intermediates during the aggregation, which could further facilitate domain swapping to form amyloid fibrils. The 1D ¹H and 2D ¹H-¹³C HSQC nuclear magnetic resonance (NMR) spectra profiling through different time points of fibrillation reveal that there may be some other species present along with the dimer during aggregation which contribute to different trends for the intensity of protons in the spectral peaks. Diffusion NMR reveals changes in the mobility of the dimeric species during the process of aggregation, indicating that the dimer gives rise to other lower molecular weight species midway during aggregation, which further add up to form the oligomers and amyloid fibrils successively. The present work is a preliminary study which explores the possibility of utilizing biophysical methods to gain atomistic level insights into the different stages of aggregation.

Chemical Exchange of Hydroxyl Groups in Lipidic Cubic Phases Characterized by NMR

Proton transportation in proximity to the lipid bilayer membrane surface, where chemical exchange represents a primary pathway, is of significant interest in many applications including cellular energy turnover underlying ATP synthesis, transmembrane mobility, and transport. Lipidic inverse bicontinuous cubic phases (LCPs) are unique membrane structures formed via the spontaneous self-assembly of certain lipids in an aqueous environment. They feature two networks of water channels, separated by a single lipid bilayer which approximates the geometry of a triply periodic minimal surface. When composed of monoolein, the LCP bilayer features two glycerol hydroxyl groups at the lipid-water interface which undergo exchange with water. Depending on the conditions of the aqueous solution used in the formation of LCPs, both resonances of the glycerol hydroxyl groups may be observed by solution ¹H NMR. In this study, PFG-NMR and 1D EXSY were employed to gain insight into chemical exchange between the monoolein hydroxyl groups and water in LCPs. Results including the relative population of hydroxyl protons in exchange with water for a number of LCPs at different hydration levels and the exchange rate constants at 35 wt % hydration are reported. Several technical aspects of PFG-NMR and EXSY-NMR for the characterization of chemical exchange in LCPs are discussed, including an alternative way to analyze PFG-NMR data of exchange systems which overcomes the inherent low sensitivity at high diffusion encoding.

High-Resolution Diffusion Measurements of Proteins by NMR under Near-Physiological Conditions

Measuring the translational diffusion of proteins under physiological conditions can be very informative, especially when multiple diffusing species can be distinguished. Diffusion NMR or diffusion-ordered spectroscopy (DOSY) is widely used to study molecular diffusion, where protons are used as probes, which can be further edited by the proton-attached heteronuclei to provide additional resolution. For example, the combination of the backbone amide protons (¹H^N) to measure diffusion with the well-resolved ¹H/¹⁵N correlations has afforded high-resolution DOSY experiments. However, significant amide-water proton exchange at physiological temperature and pH can affect the accuracy of diffusion data or cause complete loss of DOSY signals. Although aliphatic protons do not exchange with water protons, and thus are potential probes to measure diffusion rates, ¹H/¹³C correlations are often in spectral overlap or masked by the water signal, which hampers the use of these correlations. In this report, a method was developed that separates the nuclei used for diffusion (α protons, ¹H^α) and those used for detection (¹H/¹⁵N and ¹³C'/¹⁵N correlations). This approach enables high-resolution diffusion measurements of polypeptides in a mixture of biomolecules, thereby providing a powerful tool to investigate coexisting species under physiologically relevant conditions.

Protein structural changes characterized by high-pressure, pulsed field gradient diffusion NMR spectroscopy

Pulsed-field gradient NMR spectroscopy is widely used to measure the translational diffusion and hydrodynamic radius (R_h) of biomolecules in solution. For unfolded proteins, the R_h provides a sensitive reporter on the ensemble-averaged conformation and the extent of polypeptide chain expansion as a function of added denaturant. Hydrostatic pressure is a convenient and reversible alternative to chemical denaturants for the study of protein folding, and enables NMR measurements to be performed on a single sample. While the impact of pressure on the viscosity of water is well known, and our water diffusivity measurements agree closely with theoretical expectations, we find that elevated pressures increase the R_h of dioxane and other small molecules by amounts that correlate with their hydrophobicity, with parallel increases in rotational friction indicated by ¹³C longitudinal relaxation times. These data point to a tighter coupling with water for hydrophobic surfaces at elevated pressures. Translational diffusion measurement of the unfolded state of a pressure-sensitized ubiquitin mutant (VA2-ubiquitin) as a function of hydrostatic pressure or urea concentration shows that R_h values of both the folded and the unfolded states remain nearly invariant. At ca 23 Å, the R_h of the fully pressure-denatured state is essentially indistinguishable from the urea-denatured state, and close to the value expected for an idealized random coil of 76 residues. The intrinsically disordered protein (IDP) α-synuclein shows slight compaction at pressures above 2 kbar. Diffusion of unfolded ubiquitin and α-synuclein is significantly impacted by sample concentration, indicating that quantitative measurements need to be carried out under dilute conditions.

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.

Revealing Accessibility of Cryptic Protein Binding Sites within the Functional Collagen Fibril

Fibrillar collagens are the most abundant proteins in the extracellular matrix. Not only do they provide structural integrity to all of the connective tissues in the human body, but also their interactions with multiple cell receptors and other matrix molecules are essential to cell functions, such as growth, repair, and cell adhesion. Although specific binding sequences of several receptors have been determined along the collagen monomer, processes by which collagen binding partners recognize their binding sites in the collagen fibril, and the critical driving interactions, are poorly understood. The complex molecular assembly of bundled triple helices within the collagen fibril makes essential ligand binding sites cryptic or hidden from the molecular surface. Yet, critical biological processes that require collagen ligands to have access to interaction sites still occur. In this contribution, we will discuss the molecular packing of the collagen I fibril from the perspective of how collagen ligands access their known binding regions within the fibril, and we will present our analysis of binding site accessibility from the fibril surface. Understanding the basis of these interactions at the atomic level sets the stage for developing drug targets against debilitating collagen diseases and using collagen as drug delivery systems and new biomaterials.

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.

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.

NMR and molecular recognition. The application of ligand-based NMR methods to monitor molecular interactions

NMR allows the monitoring of molecular recognition processes in solution. Nowadays, a plethora of NMR methods are available to deduce the key features of the interaction from both the ligand or the receptor points of view.

Protein folding on the ribosome studied using NMR spectroscopy

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity.

EFFECT OF pH ON STRUCTURE AND STABILITY OF COLLAGEN-LIKE PEPTIDE: INSIGHT FROM MOLECULAR DYNAMICS SIMULATION

Molecular dynamics simulations were carried out to investigate the effect of pH on structure and stability of collagen-like peptide. All simulations were performed using the consistent valence force field (CVFF) molecular mechanical force field and isothermal-isobaric ensemble (NPT). The initial geometries of the collagen-like peptide were from an X-ray crystallographic structure. Some analyses from the molecular dynamics trajectories have been completed. The results show that the diameter of collagen-like peptide increases and the volume swells obviously in basic environment; however, the size of peptide changes slightly in acidic environment. The stability of collagen-like peptide decreases in acid and basic environment comparing to neutral environment based on root mean square deviation (RMSD). The number of hydrogen bond formed by peptide has a tendency to decrease in both acidic and basic environment. The average of intra-molecular H-bond is minimal under basic condition, and the average of inter-molecular H-bond between amino acid residues and water molecules is minimal under acid condition. The radial distribution function (RDF) shows that side-chain oxygen atoms are easier to form hydrogen bonds with water than side-chain nitrogen atoms. The interaction of various amino acid residues with water is position dependent. Distance between two triple helices increases markedly under highly basic condition, but changes slightly under highly acidic condition.

Osteogenesis imperfecta model peptides: incorporation of residues replacing Gly within a triple helix achieved by renucleation and local flexibility

Missense mutations, which replace one Gly with a larger residue in the repeating sequence of the type I collagen triple helix, lead to the hereditary bone disorder osteogenesis imperfecta (OI). Previous studies suggest that these mutations may interfere with triple-helix folding. NMR was used to investigate triple-helix formation in a series of model peptides where the residue replacing Gly, as well as the local sequence environment, was varied. NMR measurement of translational diffusion coefficients allowed the identification of partially folded species. When Gly was replaced by Ala, the Ala residue was incorporated into a fully folded triple helix, whereas replacement of Gly by Ser or Arg resulted in the presence of some partially folded species, suggesting a folding barrier. Increasing the triple-helix stability of the sequence N-terminal to a Gly-to-Ser replacement allowed complete triple-helix folding, whereas with the substitution of Arg, with its large side chain, the peptide achieved full folding only after flexible residues were introduced N-terminal to the mutation site. These studies shed light on the factors important for accommodation of Gly mutations within the triple helix and may relate to the varying severity of OI.

Methods to determine slow diffusion coefficients of biomolecules: applications to Engrailed 2, a partially disordered protein

We present new NMR methods to measure slow translational diffusion coefficients of biomolecules. Like the heteronuclear stimulated echo experiment (XSTE), these new methods rely on the storage of information about spatial localization during the diffusion delay as longitudinal polarization of nuclei with long T(1) such as nitrogen-15. The new BEST-XSTE sequence combines features of Band-selective Excitation Short-Transient (BEST) and XSTE methods. By avoiding the saturation of all protons except those of amide groups, one can increase the sensitivity by 45% in small proteins. The new experiment which combines band-Selective Optimized Flip-Angle Short-Transient with XSTE (SOFAST-XSTE) offers an alternative when very short recovery delays are desired. A modification of the HSQC-edited version of the XSTE experiment offers enhanced sensitivity and access to higher resolution in the indirect dimension. These new methods have been applied to detect changes in diffusion coefficients due to dimerization or proteolysis of Engrailed 2, a partially disordered protein.

How stable is a collagen triple helix? An ab initio study on various collagen and beta-sheet forming sequences

Collagen forms the well characterized triple helical secondary structure, stabilized by interchain H-bonds. Here we have investigated the stability of fully optimized collagen triple helices and beta-pleated sheets by using first principles (ab initio and DFT) calculations so as to determine the secondary structure preference depending on the amino acid composition. Models composed of a total of 18 amino acid residues were studied at six different amino acid compositions: (i) L-alanine only, (ii) glycine only, (iii) L-alanines and glycine, (iv) L-alanines and D-alanine, (v) L-prolines with glycine, (vi) L-proline, L-hydroxyproline, and glycine. The last two, v and vi, were designed to mimic the core part of collagen. Furthermore, ii, iii, and iv model the binding and/or recognition sites of collagen. Finally, i models the G-->A replacement, rare in collagen. All calculated structures show great resemblance to those determined by X-ray crystallography. Calculated triple helix formation affinities correlate well with experimentally determined stabilities derived from melting point (T(m)) data of different collagen models. The stabilization energy of a collagen triple helical structure over that of a beta-pleated sheet is 2.1 kcal mol(-1) per triplet for the [(-Pro-Hyp-Gly-)(2)](3) collagen peptide. This changes to 4.8 kcal mol(-1) per triplet of destabilization energy for the [(-Ala-Ala-Gly-)(2)](3) sequence, known to be disfavored in collagen. The present study proves that by using first principles methods for calculating stabilities of supramolecular complexes, such as collagen and beta-pleated sheets, one can obtain stability data in full agreement with experimental observations, which envisage the applicability of QM in molecular design.

Natural and artificial cystine knots for assembly of homo- and heterotrimeric collagen models

Native collagens are molecules that are difficult to handle because of their high tendency towards aggregation and denaturation. It was discovered early on that synthetic collagenous peptides are more amenable to conformational characterization and thus can serve as useful models for structural and functional studies. Single-stranded collagenous peptides of high propensity to self-associate into triple-helical trimers were used for this purpose as well as interchain-crosslinked homotrimers assembled on synthetic scaffolds. With the growing knowledge of the biosynthetic pathways of natural collagens and the importance of their interchain disulfide crosslinks, which stabilize the triple-helical structure, native as well as de novo designed cystine knots have gained increasing attention in the assembly of triple-stranded collagen peptides. In addition, natural sequences of collagens were incorporated in order to biophysically characterize their functional epitopes. This review is focused on the methods developed over the years, and future perspectives for the production of collagen-mimicking synthetic and recombinant triple-helical homo- and heterotrimers.

Computer optimized spectral aliasing in the indirect dimension of (1)H-(13)C heteronuclear 2D NMR experiments. A new algorithm and examples of applications to small molecules

A new algorithm for optimizing spectral width in the indirect dimension of heteronuclear 2D experiments is introduced. It takes a list of carbon chemical shifts as input and calculates the optimal spectral width and number of time increments to use in the carbon dimension of 2D experiments such as HSQC, HMBC, etc. When using optimized conditions where signals are better distributed along the carbon dimension, the number of time increments needed to resolve all of the signals is reduced by one to two orders of magnitude. This decreases the experimental time by the same factors and makes the acquisition of spectra such as HSQC-TOCSY, HSQC-NOESY, etc. more practical. The new algorithm allows users to limit the maximal t(1) evolution time when relaxation is a concern, and can take lists of carbons that do not need to be resolved. For any carbon, insights regarding the position of signals in the proton dimension increase the efficiency of the optimization by allowing the overlap of pairs of carbons with incompatible proton dispersions. The application of a second optimization using a fully-resolved spectrum as a source of proton dispersion for the carbons allows the number of time increments to be reduced further. Application to cyclosporine A shows that the time taken to acquire fully resolved HSQC spectra can be 126 times less than would be required in a full-width spectrum with the same resolution. The most interesting applications concern experiments where series of HSQC-based experiments have to be acquired, for example in relaxation time measurements. It is shown that the acquisition of quickly acquired series of selective-TOCSY-HSQC can facilitate assignment in carbohydrates. Computer-optimized spectral aliasing (COSA) generally requires no modification of the pulse sequence and can therefore be easily applied by non specialists.

The Cold Denatured State Is Compact but Expands at Low Temperatures: Hydrodynamic Properties of the Cold Denatured State of the C-terminal Domain of L9

A point mutation of a small globular protein, the C-terminal domain of L9 destabilizes the protein and leads to observable cold-denaturation at temperatures above zero. The cold denatured state is in slow exchange with the native state on the NMR time scale, and this allows the hydrodynamic properties of the cold unfolded state and the native state to be measured under identical conditions using pulsed-field gradient NMR diffusion measurements. This provides the first experimental measurement of the hydrodynamic properties of a cold unfolded protein and its folded form under identical conditions. Hydrodynamic radii of the cold-induced unfolded states were measured for a set of temperatures ranging from 2 degrees C to 25 degrees C at pD 6.6 in the absence of denaturant. The cold unfolded state is compact compared to the urea or acid unfolded state and a trend of increasing radii of hydration is observed as the temperature is lowered. These observations are confirmed by experiments on the same protein at pD 8.0, where it is more stable, in the presence of a modest concentration of urea. The expansion of the cold-denatured state at lower temperatures is consistent with the temperature dependence of hydrophobic interactions.

NMR Diffusion Measurements in Complex Mixtures Using Constant-Time-HSQC-IDOSY and Computer-Optimized Spectral Aliasing for High Resolution in the Carbon Dimension

A new 3D pulse sequence for NMR diffusion measurements in complex mixtures is presented. It is based on the constant-time (CT) HSQC experiment and combines diffusion delay with the carbon evolution time. This combination has great potential to obtain high resolution in the carbon dimension. When using classical sampling of the carbon dimension, maximal resolution would require a large number of time increments, leading to unrealistically long acquisition times. The application of computer-optimized spectral aliasing allows one to reduce the number of time increments and the total acquisition time by 1-2 orders of magnitude by taking advantage of the information content of 1D carbon spectra, HSQC experiments, or both. With the new CT-HSQC-IDOSY experiment, the diffusion rates of the six anomers present in a 0.1 M D2O solution of glucose, maltose, and maltotriose could be obtained at natural abundance in 8 h with standard deviations below 5%.

Diffusion NMR spectroscopy in supramolecular and combinatorial chemistry: an old parameter--new insights

Intermolecular interactions in solution play an important role in molecular recognition, which lies at the heart of supramolecular and combinatorial chemistry. Diffusion NMR spectroscopy gives information over such interactions and has become the method of choice for simultaneously measuring diffusion coefficients of multicomponent systems. The diffusion coefficient reflects the effective size and shape of a molecular species. Applications of this technique include the estimation of association constants and mapping the intermolecular interactions in multicomponent systems as well as investigating aggregation, ion pairing, encapsulation, and the size and structure of labile systems. Diffusion NMR spectroscopy can also be used to virtually separate mixtures and screen for specific ligands of different receptors, and may assist in finding lead compounds.

Identification of partially disordered peptide intermediates through residue-specific NMR diffusion measurements

It is technically challenging to detect low-population partially disordered species that are in equilibrium with the folded and unfolded states. Residue-specific translational diffusion experiments measured by pulsed field gradient NMR have been used to detect the presence, and define the conformation, of such equilibrium intermediates. The experiment is demonstrated for equilibrium solutions of related triple helical peptides that model a small region of type I collagen with and without a mutation known to cause osteogenesis imperfecta. The data show that residue-specific diffusion coefficients of an interconverting trimer to monomer system can allow discrimination between a simple two-state model and more complex multistate models involving partially disordered intermediates.

Rapid 1H{13C}-Resolved Diffusion and Spin-Relaxation Measurements by NMR Spectroscopy

Hadamard-encoded heteronuclear-resolved NMR diffusion and relaxation measurements allow overlapping signal decays to be resolved with substantially shorter measuring times than are generally associated with 2D heteronuclear cross-correlation experiments. Overall measuring time requirements can be reduced by approximately an order of magnitude, compared to typical 2D heteronuclear single-quantum correlation-resolved diffusion or relaxation measurements. Specifically, in cases where chemical shift correlation information provides enhanced spectral resolution, the use of Hadamard encoding can be used to overcome uniqueness challenges that are associated with the analysis of concurrent dynamic processes and the extraction of time constants from overlapping exponential signal decays. This leads to substantially improved resolution of similar time constants than can be achieved solely through the use of post-acquisition processing techniques. In the ideal case of complete spectral separation of the signal decays, the usual constraint that time constants must be sufficiently different to resolve by exponential analysis can be circumvented entirely. Hadamard-based pulse sequences have been used to determine 1H[13C]-resolved diffusion coefficients and spin-relaxation time constants for the chemically similar components of an aqueous solution of ethanol, glycerol, and poly(ethylene glycol), and a dye-containing block-copolymer solution, which exhibit significant spectral overlap in their 1H NMR spectra.

Stability Junction at a Common Mutation Site in the Collagenous Domain of the Mannose Binding Lectin

Missense mutations in the collagen triple-helix that replace one of the required Gly residues in the (Gly-Xaa-Yaa)(n)() repeating sequence have been implicated in various disorders. Although most hereditary collagen disorders are rare, a common occurrence of a Gly replacement mutation is found in the collagenous domain of mannose binding lectin (MBL). A Gly --> Asp mutation at position 54 in MBL is found at a frequency as high as 30% in certain populations and leads to increased susceptibility to infections. The structural and energetic consequences of this mutation are investigated by comparing a triple-helical peptide containing the N-terminal Gly-X-Y units of MBL with the homologous peptide containing the Gly to Asp replacement. The mutation leads to a loss of triple-helix content but only a small decrease in the stability of the triple-helix (DeltaT(m) approximately 2 degrees C) and no change in the calorimetric enthalpy. NMR studies on specifically labeled residues indicate the portion of the peptide C-terminal to residue 54 is in a highly ordered triple-helix in both peptides, while residues N-terminal to the mutation site have a weak triple-helical signal in the parent peptide and are completely disordered in the mutant peptide. These results suggest that the N-terminal triplet residues are contributing little to the stability of this peptide, a hypothesis confirmed by the stability and enthalpy of shorter peptides containing only the region C-terminal to the mutation site. The Gly to Asp replacement at position 54 in MBL occurs at the boundary of a highly stable triple-helix region and a very unstable sequence. The junctional position of this mutation minimizes its destabilizing effect, in contrast with the significant destabilization seen for Gly replacements in peptides modeling collagen diseases.

Monitoring protein folding at atomic resolution

Elucidation of the mechanisms by which proteins fold from disordered conformations to their unique native conformations is one of the most challenging tasks facing structural biologists. Understanding the mechanism(s) of protein folding involves the characterization of all structural species that occur in the protein-folding reaction. Nuclear magnetic resonance (NMR) spectroscopy is a powerful and versatile technique that provides an avenue to investigate the structures of the various conformational states at the residue level along the protein-folding reaction coordinate. In this Account, we provide a comprehensive review of the recent progress on the applications of NMR to monitor equilibrium and kinetic conformational states of the protein-folding reaction.

Interactions of charged porphyrins with nonionic triblock copolymer hosts in aqueous solutions

The extent and locus of solubilization of guest and self-assembling surfactant host molecules in aqueous solutions are influenced by a variety of hydrophobic and hydrophilic interactions, as well as by more specific interactions between the various species present. By using a combination of two-dimensional heteronuclear 13C[1H] NMR correlation experiments with pulsed-gradient NMR diffusion and proton cross-relaxation measurements, the locations and distributions of porphyrin guest molecules have been established unambiguously with respect to the hydrophobic and hydrophilic moieties of a triblock copolymer species in solution. The interactions of tetra(4-sulfonatophenyl)porphyrin with the poly(propylene oxide) (PPO) and the poly(ethylene oxide) (PEO) segments of amphiphilic PEO-PPO-PEO triblock copolymer species have been measured as functions of solution conditions, including temperature and pH. The porphyrin/PEO-PPO-PEO interactions are established to be selective and adjustable according to the different temperature-dependent hydrophilicities or hydrophobicities of the PEO and PPO triblock copolymer components. Furthermore, such interactions influence the self-assembly properties of the block-copolymer amphiphiles in solution by stabilizing molecular porphyrin/PEO-PPO-PEO complexes well above the critical micellization temperature of the triblock copolymer species under otherwise identical conditions.

A (4R)- or a (4S)-Fluoroproline Residue in Position Xaa of the (Xaa-Yaa-Gly) Collagen Repeat Severely Affects Triple-Helix Formation

The triple-helical fold of collagen requires the presence of a glycine residue at every third position in the peptide sequence and is stabilized by proline and (4R)-4-hydroxyproline residues in positions Xaa and Yaa of the (Xaa-Yaa-Gly) triplets, respectively. Regular down/up puckering of these Xaa/Yaa residues is possibly responsible for the tight packing of the three peptide strands, which have a polyproline-II-like structure, into the supercoiled helix. (4R)-Configured electronegative substituents such as a hydroxy group or a fluorine substituent on the pyrrolidine ring of the residue in the Yaa position favor the up pucker and thus significantly stabilize the triple helix. A similar effect was expected from the corresponding (4S)-isomers in the Xaa positions, but the opposite effect has been observed with (4S)-hydroxyproline, a result that has been speculatively attributed to steric effects. In this study, (4R)- and (4S)-fluoroproline residues were introduced into the Xaa position and potential steric effects were thus avoided. Contrary to expectations, (4S)-fluoroproline prevents triple-helix formation, whereas (4R)-fluoroproline stabilizes the polyPro II conformation, but without supercoiling of the three strands. The latter observation suggests that folding of the single chains into a polyproline II helix is not directly associated with triple helix formation and that fine tuning of van der Waals contacts, electrostatic interactions, and stereoelectronic effects is required for optimal packing into a triple helix.

Diffusion measurements by electrospray mass spectrometry for studying solution-phase noncovalent interactions

This study describes a novel approach for monitoring noncovalent interactions in solution by electrospray mass spectrometry (ESI-MS). The technique is based on measurements of analyte diffusion in solution. Diffusion coefficients of a target macromolecule and a potential low molecular weight binding partner are determined by measuring the spread of an initially sharp boundary between two solutions of different concentration in a laminar flow tube (Taylor dispersion), as described in Rapid Commun. Mass Spectrom. 2002, 16, 1454-1462. In the absence of noncovalent interactions, the measured ESI-MS dispersion profiles are expected to show a gradual transition for the macromolecule and a steep transition for the low molecular weight compound. However, if the two analytes form a noncovalent complex in solution the dispersion profiles of the two species will be very similar, since the translational diffusion of the small compound is determined by the slow Brownian motion of the macromolecule. In contrast to conventional ESI-MS-based techniques for studying noncovalent complexes, this approach does not rely on the preservation of solution-phase interactions in the gas phase. On the contrary, "harsh" conditions at the ion source are required to disrupt any potential gas- phase interactions between the two species, such that their dispersion profiles can be monitored separately. The viability of this technique is demonstrated in studies on noncovalent heme-protein interactions in myoglobin. Tight noncovalent binding is observed in solutions of pH 10, both in the absence and in the presence of 30% acetonitrile. In contrast, a significant disruption of the noncovalent interactions is seen at an acetonitrile content of 50%. Under these conditions, the diffusion coefficient of heme in the presence of myoglobin is only slightly lower than that of heme in a protein-free solution. A breakdown of the noncovalent interactions is also observed in aqueous solution of pH 2.4, where myoglobin is known to adopt an acid-unfolded conformation.

Collagen triple helix formation can be nucleated at either end

The directional dependence of folding rates for rod-like macromolecules such as parallel alpha-helical coiled-coils, DNA double-helices, and collagen triple helices is largely unexplored. This is mainly due to technical difficulties in measuring rates in different directions. Folding of collagens is nucleated by trimeric non-collagenous domains. These are usually located at the COOH terminus, suggesting that triple helix folding proceeds from the COOH to the NH(2) terminus. Evidence is presented here that effective nucleation is possible at both ends of the collagen-like peptide (Gly-Pro-Pro)(10), using designed proteins in which this peptide is fused either NH(2)- or COOH-terminal to a nucleation domain, either T4-phage foldon or the disulfide knot of type III collagen. The location of the nucleation domain influences triple-helical stability, which might be explained by differences in the linker sequences and the presence or absence of repulsive charges at the carboxyl-terminal end of the triple helix. Triple helical folding rates are found to be independent of the site of nucleation and consistent with cis-trans isomerization being the rate-limiting step.