Biomedical subjects

C M Dobson

Publications and source records attributed to C M Dobson.

At least 163 records · Page 9Linked to original sources

PubMed1994

The refolding of human lysozyme: a comparison with the structurally homologous hen lysozyme.

Pulsed hydrogen exchange labeling has been used in conjunction with circular dichroism in the near and far UV to study the refolding of human lysozyme from its guanidinium chloride denatured state. Human lysozyme differs in sequence by 51 residues and one insertion from the hen protein, which has previously been studied under identical conditions by similar methods [Radford, S. E., Dobson, C. M., & Evans, P. A. (1992) Nature 358, 302-307]. The two proteins show marked differences in their folding kinetics. First, the overall rate of refolding of human lysozyme is 4-fold faster than that of the hen protein. Second, although protection of amides in the alpha-domain develops faster than that of amides in the beta-domain in both proteins, unlike hen lysozyme stabilization of the secondary structural elements of the alpha-domain in human lysozyme does not occur in a fully cooperative manner. Rather, amide hydrogens in two alpha-helices located near to the N-terminus and in the 3(10) helix close to the C-terminus of the protein are protected from exchange significantly faster than those in the remaining two alpha-helices in the alpha-domain of the protein. Third, stopped flow CD measurements show that both proteins develop extensive secondary structure during the dead time of these experiments (ca. 2 ms); this is accompanied by formation of tertiary interactions, probably involving tryptophan residues, only in the human enzyme. These results suggest that although the fundamental folding process is similar in the two proteins, human lysozyme differs in that it forms a stable subdomain involving the two N-terminal alpha-helices and the C-terminal 3(10) helix in the first few milliseconds of folding, and that at least some tryptophan residues are ordered before the formation of the native state. This indicates that the details of the folding of homologous proteins may differ as a consequence of amino acid substitutions and suggests that the study of mutant and variant proteins can provide clues as to the determinants of folding.

Amino Acid Sequence↗

PubMed1994

Tertiary interactions in the folding pathway of hen lysozyme: kinetic studies using fluorescent probes.

The refolding kinetics of hen lysozyme have been studied using a range of fluorescent probes. These experiments have provided new insight into the nature of intermediates detected in our recent hydrogen-exchange labeling studies [Radford, S.E., et al. (1992) Nature 358, 302-307], which were performed under the same conditions. Protection from exchange results primarily from the development of stabilizing side-chain interactions, and the fluorescence studies reported here have provided a new perspective on this aspect of the refolding process. The intrinsic fluorescence of the six tryptophan residues and its susceptibility to quenching by iodide have been used to monitor the development of hydrophobic structure, and these studies have been complemented by experiments involving binding to a fluorescent hydrophobic dye 1-anilino-naphthalenesulfonic acid (ANS). Formation of fixed tertiary interactions of aromatic residues has been monitored by near-UV circular dichorism, while development of a competent active site has been probed by binding to a competitive inhibitor bearing a fluorescent label, 4-methylumbelliferyl-N,N'-diacetyl-beta-chitobiose. The combination of these techniques has enabled us to monitor the development both of the hydrophobic core of the protein and of interactions between the two folding domains. If the behavior of the tryptophans is representative of the hydrophobic residues of the protein in general, it seems that collapse is already substantial in species formed within the first few milliseconds of refolding and is highly developed in later intermediates which nonetheless appear to lack many fixed tertiary interactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1994

Analysis of the solution structure of human interleukin-4 determined by heteronuclear three-dimensional nuclear magnetic resonance techniques.

Human interleukin-4 (IL-4) is a member of the family of haemopoietic cytokines that modulate cell proliferation and differentiation within the immune system. It has a four-helix-bundle structure, and possesses a high degree of mobility in certain regions, notably in the two long loops running the length of the bundle in its up-up-down-down topology. Information from a variety of three-dimensional heteronuclear NMR experiments, including chemical shifts, coupling constants and NOE data, is analysed in terms of the solution structure of IL-4. In addition, structure calculations with and without specific restraints such as hydrogen bond location or torsion angle restrictions are compared in the light of the dynamic behaviour of the polypeptide chain. Particular emphasis is placed on defining the lengths and positions of secondary structure elements, and on the likely structural preferences within the less well ordered loop regions. The overall topology of IL-4 is compared with those defined in recent structure determinations of related proteins. This analysis is combined with recent mutagenesis data to propose a possible mode of interaction of IL-4 with its receptor.

Crystallography, X-Ray↗

PubMed1994

Amide hydrogen exchange in a highly denatured state. Hen egg-white lysozyme in urea.

The amide hydrogen exchange behaviour of hen egg-white lysozyme denatured in 8 M urea has been studied at pH 2.0, 20 degrees C. The observed exchange rates have been compared with those predicted for the same residues in a random coil conformation using recently published parameters for side-chain inductive and temperature effects on exchange catalysis. The protection factors for exchange obtained in this way were found to be close to unity, with 41 of the 61 residues that could be followed having protection factors less than 2. No protection factor was greater than 5. In addition, previous data for hen lysozyme denatured thermally and for a three-disulphide derivative, CM6-127 lysozyme, denatured at pH 2.0 have been reanalysed using the new reference parameters, and the protection factors were found to be similar to those of hen lysozyme denatured in 8 M urea. Thus, although 1H NMR and far UV CD spectroscopy suggest that considerable deviations from random coil behaviour occur in these denatured states, such residual structure is insufficient to protect amide hydrogens significantly against exchange. This behaviour contrasts with that of a partly folded state of hen lysozyme denatured in trifluoroethanol and with that of the molten globule state of a homologous protein, guinea pig alpha-lactalbumin. Here protection factors for many amide hydrogens exceed 30 and belong to residues located in continuous regions of the amino acid sequence, indicating the presence of persistent structure. The study of hydrogen exchange in substantially denatured states of a protein, therefore, provides a basis for the interpretation of protection factors in partially folded states.

Amides↗

PubMed1994

Unfolding studies of the protease domain of urokinase-type plasminogen activator: the existence of partly folded states and stable subdomains.

The domain structure and the stability against thermal and chemical denaturation of urokinase-type plasminogen activator (u-PA) have been investigated by NMR spectroscopy and differential scanning calorimetry (DSC). At least five structurally autonomous regions of this three-domain protein have been found to exist. Two of these are the EGF-like and the kringle domains; the others are all within the third domain, which is a serine protease. The latter undergoes three unfolding transitions in its enzymatically active form. Reaction with a specific affinity label (L-Glu-L-Gly-L-Arg-chloromethyl ketone) to produce an inactivated protein results in a stabilization of the structure involved in two of these transitions, and an increase in cooperativity to give a domain which unfolds in two, not three, distinct steps. These are attributed to the denaturation of the two major subdomains of the protease structure. One of the subdomains has exceptional stability, being unfolded only under extreme conditions such as 75 degrees C at pH 2.5 or 4 M GuDCl at pH 4.5 and 29 degrees C. This region has been identified by isolation and characterization of a fragment (residues Ile-159 to Thr-277) obtained by limited proteolysis with thermolysin under conditions where the protease domain was partly unfolded. The NMR data are consistent with this stable region being at the N-terminus of the protein and indicate that its structure and stability are similar to those of the corresponding region of the native protein. These results support the idea that the u-PA protease domain has structural resemblance to the digestive serine proteases, but that stabilizing interactions within the structure can differ significantly between a group of homologous proteins.

Affinity Labels↗

PubMed1994

Solution structure of the kringle domain from urokinase-type plasminogen activator.

The solution structure of the kringle domain from urokinase-type plasminogen activator (u-PA) has been determined using 1H nuclear magnetic resonance spectroscopy and dynamical simulated annealing calculations. A total of 35 structures, 20 generated using a distance geometry method prior to simulated annealing and 15 generated using initial random phi, psi values, have been calculated based on 946 experimental nuclear Overhauser effect distance constraints and 48 dihedral angle constraints. Excluding the N- and C-terminal residues (-1 to 12, 77 to 82) and a number of surface residues (M18, G19, S42, D55 to R60, G67) that are disordered or flexible, the root mean square deviation values from the mean structure are 0.49(+/- 0.14) A and 0.65(+/- 0.16) A for the backbone atoms, and 1.03(+/- 0.21) A and 1.39(+/- 0.24) A for all heavy atoms, for the two sets of structures, respectively. An extended binding site for anionic polysaccharides such as heparin has been located on a relatively flat facet of the molecule, involving three consecutive arginines, R57, R58 and R60 (there is a deletion at site 59 of the consensus sequence), which form a cationic triad facing the solvent, and two histidines, H37 and H40, at the opposite end of the molecule. Comparison between the u-PA kringle structure and the crystal and NMR solution structures of tissue-type plasminogen activator kringle 2 has shown that the two proteins have similar global folds but demonstrate a number of local differences.

Amino Acid Sequence↗

PubMed1994

1H nuclear magnetic resonance studies of hen lysozyme-N-acetylglucosamine oligosaccharide complexes in solution. Application of chemical shifts for the comparison of conformational changes in solution and in the crystal.

Two-dimensional 1H nuclear magnetic resonance spectroscopy has been used to examine the complexes formed in solution between hen egg-white lysozyme and N-acetylglucosamine (GlcNAc) oligosaccharides. Changes in chemical shift have been measured for resonances of the majority of residues of lysozyme on binding the monomer, dimer and trimer of GlcNAc. The three inhibitors induce very similar changes in chemical shift, and these increase slightly with the length of the oligosaccharide. The largest changes are confined principally to the vicinity of site C in the active site cleft of the enzyme. These changes in chemical shift have been compared with differences in the ring current chemical shifts calculated from the crystal structures of unbound and GlcNAc3 bound lysozyme. This comparison suggests that the major conformational changes of residues in the vicinity of site C of the enzyme, that are caused by the binding of GlcNAc3, observed in the diffraction studies are at least consistent with the changes that occur in solution. Small changes in chemical shift are observed in the enzyme in regions remote from the active site, which indicate that the effects of inhibitor binding are felt throughout the enzyme. These changes in chemical shift correlate to a lesser extent than those near site C with the changes in chemical shift predicted from changes in conformation observed in the crystal structures. The results illustrate that chemical shifts are useful in assessing the significance of small conformational changes in proteins, although the usefulness of this approach will be limited by the resolution of the crystallographic structures, as well as the uncertainties in the origins of the chemical shift. Although conformational changes in site C account for many of the changes in the NMR spectrum of lysozyme, evidence is, however, presented for multiple binding sites for the GlcNAc oligosaccharides in solution, perhaps involving partial occupancy of site D.

Acetylglucosamine↗

PubMed1994

Characterization of a trifluoroethanol-induced partially folded state of alpha-lactalbumin.

The protein alpha-lactalbumin exists in a partially folded molten globule state at pH 2.0, the A state. This state is believed to be compact, possessing a similar amount of secondary structure to the native state but having a flexible tertiary structure comprised mainly of non-specific hydrophobic clustering of residues. Addition of trifluoroethanol (TFE) to bovine, human and guinea pig alpha-lactalbumin at pH 2.0 has been found in each case to induce a conformational transition in the A state as monitored by circular dichroism, nuclear magnetic resonance chemical shifts, and 1-anilinonaphthalene-8-sulphonate binding. The mid-point of this transition is near 15% (v/v) TFE and is effectively complete by 50% (v/v) TFE at 315 K. Far ultraviolet circular dichroism ellipticities at 208 nm and 220 nm, usually taken as a measure of the degree of helical character, are substantially more negative in the TFE state than in the A state. Furthermore, backbone amide protons protected from solvent exchange in the A state are generally at least as strongly protected in the TFE state; patterns of protection appear similar in the two states and include at least part of both the B and C alpha-helices. One major difference from the A state is nevertheless evident: the ability to bind the fluorescent probe 1-anilinonaphthalene-8-sulphonate, characteristic of molten globule states, is lost in the TFE state. Like the A state, the TFE state of alpha-lactalbumin shows little chemical shift dispersion of side-chain resonances. Extensive line broadening in the nuclear magnetic resonance spectra, characteristic of slow conformational averaging in the A state, is, however, much reduced in the TFE state. The line narrowing observed in the TFE state has made it possible to obtain directly sequence-specific assignments for about 25% of the 123 residues of bovine alpha-lactalbumin in 50% (v/v) TFE. Two helices are amongst regions of structure so far identified from short-range backbone nuclear Overhauser enhancement (NOE) connectivities in two-dimensional spectra of the TFE state. One of the helices (residues 86 to 96) corresponds to the C-helix in the native structure. The other (residues 35 to 41) corresponds, however, to a region of the sequence that is not helical in the native state. The partially folded state of alpha-lactalbumin formed in TFE, therefore, supports both native and non-native secondary structure in the absence of persistent long-range tertiary structure.

Amino Acid Sequence↗

PubMed1994

Understanding how proteins fold: the lysozyme story so far.

Hen lysozyme is one of the best characterized and most studied of all proteins. Recently, we have used a range of different methods to examine the events involved in the in vitro folding pathway of this protein. In this review we show that, by combining complementary techniques, it has been possible to piece together a detailed model for the folding of this enzyme. Important questions prompted by this work are highlighted and we then propose some ideas consistent with our data, as well as those of others, which we believe begin to provide insight into one of the most intriguing of structural problems in biology--how proteins can achieve their complex native forms from disordered denatured states.

Animals↗

PubMed1994

Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR.

The pH dependence of the two-dimensional 1H nuclear magnetic resonance spectra of hen and turkey egg-white lysozymes has been recorded over the pH range 1-7. By monitoring the chemical shifts of the resonances of the various protons of ionizable residues, individual pKa values for the acidic residues have been determined for both proteins. The pKa values are displaced, with the exception of those of the residues in the active site cleft, by an average of 1 unit to low pH compared to model compounds.

Amino Acid Sequence↗

PubMed1994

Structural characterization of a highly-ordered 'molten globule' at low pH.

The characterization of unfolded and partly folded states of proteins is central to understanding protein stability and folding, as well as providing a basis for protein design. The four helix bundle-protein interleukin-4 undergoes an unfolding transition at low pH. Using heteronuclear nuclear magnetic resonance methods we show that following this transition the protein retains a highly ordered hydrophobic core in which most, but not all, of the secondary structure is preserved. Extensive disorder exists, however, in regions of polypeptide chain linking the structural elements which make up this core. We suggest that this 'highly ordered molten globule' could be indicative of the type of structures occurring late in protein folding processes, in contrast to more disordered 'molten globules' which relate to early folding intermediates.

Anilino Naphthalenesulfonates↗

PubMed1994

Comparison of four independently determined structures of human recombinant interleukin-4.

Four independent structures of human interleukin-4, two determined by nuclear magnetic resonance techniques and two by X-ray diffraction, have been compared in detail. The core of this four helix bundle protein is very similar in all the structures but there are some differences in loop regions that are known to be mobile in solution. Careful comparison of the experimental data sets and the methods of analysis of the different laboratories has provided clues to the sources of most of the differences, and also answered some general questions about the accuracy of protein structure determination by these two techniques.

Crystallography, X-Ray↗

PubMed1993

Partially folded states of equine lysozyme. Structural characterization and significance for protein folding.

Despite their homologous structure, c-type lysozymes and alpha-lactalbumins have been found to differ profoundly in their unfolding behavior, in that the alpha-lactalbumins readily enter a partially unfolded collapsed state (the "molten globule"), whereas lysozymes unfold cooperatively to a highly unfolded state. The calcium-binding property of lysozyme from equine milk provides an evolutionary link between the two families of proteins. We demonstrate here that equine lysozyme undergoes a two-stage unfolding transition upon heating or in the presence of guanidine hydrochloride that is highly dependent on the state of calcium binding. Differential scanning calorimetry shows the two transitions to be particularly well resolved in the calcium-free protein, where the first transition occurs with a midpoint at 44 degrees C at pH 4.5 or in 0.8 M GdnHCl at pH 7.5, 25 degrees C, and the second occurs near 70 degrees C at pH 4.5 or in 3.7 M GdnHCl at pH 7.5, 25 degrees C. In the presence of calcium, the first transition takes place with a midpoint of 55 degrees C or in excess of 2.5 M GdnHCl, but the parameters for the second transition remain unchanged. Fluorescence emission and UV difference absorption spectroscopy suggest that the first transition generates an intermediate state in which sequestration of some aromatic side chains from solvent has occurred whereas the second represents denaturation to a highly unfolded state. CD and 1H NMR results indicate that the intermediate state possesses extensive secondary and tertiary structure, although the latter is substantially disordered.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1993

Detection of transient protein folding populations by mass spectrometry.

Hydrogen-deuterium exchange measurements are becoming increasingly important in studies of the dynamics of protein molecules and, particularly, of their folding behavior. Electrospray ionization mass spectrometry (ESI-MS) has been used to obtain the distribution of masses within a population of protein molecules that had undergone hydrogen exchange in solution. This information is complementary to that from nuclear magnetic resonance spectroscopy (NMR) experiments, which measure the average occupancy of individual sites over the distribution of protein molecules. In experiments with hen lysozyme, a combination of ESI-MS and NMR was used to distinguish between alternative mechanisms of hydrogen exchange, providing insight into the nature and populations of transient folding intermediates. These results have helped to detail the pathways available to a protein during refolding.

Hydrogen↗

PubMed1993

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Journal Article↗

PubMed1993

Binding of a substrate analogue can induce co-operative structure in the plasmin serine-proteinase domain.

Human miniplasminogen and miniplasmin were studied by n.m.r. spectroscopy and differential scanning calorimetry (d.s.c.) in order to investigate the structural properties of the serine-proteinase domain. The d.s.c. thermograms of both miniplasminogen and non-inactivated miniplasmin at pH 4.0 can be closely fitted to two transitions, at 62 +/- 2 and 72 +/- 2 degrees C, corresponding to unfolding of the kringle 5 and proteinase domains respectively. No evidence was found, under these conditions, for non-co-operative unfolding of the proteinase domain. On inactivation of miniplasmin with an affinity label, a number of additional resonances arising from residues of the proteinase domain are observed in resolved regions of the n.m.r. spectrum. A combination of variable-temperature n.m.r. and d.s.c. has shown that part of the proteinase domain undergoes a major conformational transition on heating which is distinct from the unfolding of the remainder of the proteinase domain or the kringle 5 domain. This additional transition occurs at a temperature that depends on the nature of the affinity label present and is not observed in the absence of an inactivating agent. These results provide direct evidence for the existence of a region of the proteinase domain which, under these conditions, becomes structured only in the presence of a bound substrate.

Affinity Labels↗

PubMed1993

1H-NMR analysis of turkey egg-white lysozyme and comparison with hen egg-white lysozyme.

The complete main chain and approximately 75% of the side chain 1H-NMR assignments of the 129-residue protein, turkey egg-white lysozyme, are presented. NOE data, hydrogen-exchange rates, chemical shifts and coupling constants are reported and are indicative of a structure in solution that is essentially identical to that of the homologous hen egg-white lysozyme. The NH-alpha CH coupling constants of turkey lysozyme are compared to torsion-angle data from three crystal structures of the protein and the results are interpreted in terms of crystal-structure resolution and refinement.

Amino Acid Sequence↗

PubMed1993

Structure and stability of the molten globule state of guinea-pig alpha-lactalbumin: a hydrogen exchange study.

A partially folded state of guinea pig alpha-lactalbumin (the A-state or molten globule state), formed by denaturation at low pH, has been studied using hydrogen exchange methods. The overall distribution of exchange kinetics, measured by 1-D NMR, suggests that fewer than 20 amides in the structure are involved in highly persistent residual structure, although CD results suggest that many other parts of the chain are folded, for a significant proportion of the time, into less stable structural elements. The pH-jump experiments show that some amides that are strongly protected from exchange in the native state become freely accessible in the A-state but that conversely a majority, at least, of those that are slow to exchange in the A-state retain that protection in the native state. This suggests that the persistent structure in the A-state is native-like although the possibility that nonnative like structural elements persist cannot be eliminated. Resonance assignments for key residues in the NMR spectrum of the native state have enabled us to use the pH-jump method also to identify the majority of the most protected amides in the A-state: they are located in two hydrophobic segments, corresponding to the B- and C-helices of the native structure. This strongly suggests that the most persistent structure of the A-state includes these regions. A variety of lines of evidence, including fluorescence quenching data and, most remarkably, very effective protection from exchange of an indole NH in a tryptophan side chain, suggest that some form of hydrophobic core in the helical domain of the native structure persists in the A-state, although without the stereochemical rigidity of the native tertiary structure. The other domain of the native structure, including the beta-sheet, appears not to contain structural elements which persist to the same extent in the A-state, emphasizing that the molten globule is highly heterogeneous, in terms of the stability and specificity of both backbone and side chain interactions.

Amino Acid Sequence↗