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C M Dobson

Publications and source records attributed to C M Dobson.

At least 217 records · Page 12Linked to original sources
PubMed1990

1H NMR studies of human lysozyme: spectral assignment and comparison with hen lysozyme.

Complete main-chain (NH and alpha CH) 1H NMR assignments are reported for the 130 residues of human lysozyme, along with extensive assignments for side-chain protons. Analysis of 2-D NOESY experiments shows that the regions of secondary structure for human lysozyme in solution are essentially identical with those found previously in a similar study of hen lysozyme and are in close accord with the structure of the protein reported previously from X-ray diffraction studies in the crystalline state. Comparison of the chemical shifts, spin-spin coupling constants, and hydrogen exchange behavior are also consistent with closely similar structures for the two proteins in solution. In a number of cases specific differences in the NMR parameters between hen and human lysozymes can be correlated with specific differences observed in the crystal structures.

Amino Acid Sequence↗
PubMed1990

Hen egg white lysozyme expressed in, and secreted from, Aspergillus niger is correctly processed and folded.

We transformed Aspergillus niger with the full length cDNA gene encoding hen egg-white lysozyme (HEWL) and its secretion signal sequence. Lysozyme levels up to 12 mg/l were secreted when expression was controlled by the A. awamori glucoamylase (GAM) promoter and 1 mg/l when controlled by the A. nidulans glyceraldehyde-3-phosphate dehydrogenase (GPD) promoter. N-terminal sequence analysis of the recombinant protein indicated that the signal peptide was correctly processed by the A. niger secretory apparatus. The specific catalytic activity of the recombinant protein was identical to that of authentic hen lysozyme. The recombinant HEWL was examined by 2D 1H-NMR spectroscopy and shown to have a spectrum identical to that of authentic HEWL indicating that the protein was correctly folded.

Amino Acid Sequence↗
PubMed1989

Reversible independent unfolding of the domains of urokinase monitored by 1H NMR.

Human urinary-type plasminogen activator (urokinase) and proteolytic fragments corresponding to the kringle, EGF-kringle, and protease domains have been examined by 1H NMR spectroscopy. The intact protein shows a very well-resolved spectrum for a molecule of this size (MW 54,000), with resonance line widths not greatly increased from those of the isolated domains. On increasing the temperature, the protein at pH values close to 4 was found to undergo two distinct and reversible conformational transitions. These were identified, by comparison with spectra of the proteolytic fragments, as the unfolding of the kringle (and EGF) domains (at approximately 42 degrees C) and of a segment of the protease domain (at approximately 60 degrees C). The remaining segment of the protease domain showed persistent structure to at least 85 degrees C at pH 4; only at lower pH values could complete unfolding be achieved. The results indicate that the structures and stabilities of the isolated domains are closely similar to those in the intact protein and suggest that there is a degree of independent motion at least between the kringle and protease domains.

Amino Acid Sequence↗
PubMed1989

Dynamics of the multidomain fibrinolytic protein urokinase from two-dimensional NMR.

The recent demonstrations that thrombolytic therapy with plasminogen activators can result in substantial reductions in mortality from coronary thrombosis have generated considerable interest in the properties of fibrinolytic enzymes. Examination of the primary sequence of these proteins (which include tissue plasminogen activator, plasminogen, and urokinase) reveals that each is composed of a mosaic of domains which appear to be spatially distinct and connected by short peptide linkers. There is, however, little experimental information about the three-dimensional structure of any of the proteins, although several X-ray diffraction and NMR studies of isolated domains have been reported. Here we report two-dimensional NMR spectra of intact urokinase which are remarkably well resolved for a protein of this molecular weight. This effect is a consequence of substantial independent motion between individual domains of the protein, which overcomes the broadening effects anticipated for the slow overall tumbling rate of the intact molecule. As well as having significance for the physiological role of the protein, these results provide a direct means for the comparison of structural features determined for the isolated domains with those of the intact protein and may provide a basis for proposing or evaluating models for the overall structure of fibrinolytic proteins. Preliminary results with other proteins indicate that this approach may be generally applicable to other multidomain proteins of the fibrinolytic family.

Epidermal Growth Factor↗
PubMed1989

Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig alpha-lactalbumin.

NMR spectroscopy has been used to investigate the structure of a partially folded state of a protein, the molten globule or A-state of alpha-lactalbumin. The 1H NMR spectrum of this species differs substantially from those of both the native and fully unfolded states, reflecting the intermediate level of order. The resolution in the spectrum is limited by the widespread overlap and substantial line widths of many of the resonances. Methods have therefore been developed that exploit the well-resolved spectrum of the native protein to probe indirectly the A-state. A number of resonances of the A-state have been found to be substantially shifted from their positions in the spectrum of the unfolded state and have been identified through magnetization transfer with the native state, under conditions where the two states are interconverting. The most strongly perturbed residues in the A-state were found to be among those that form a hydrophobic core to the native structure. A number of amides were found to be highly protected from solvent exchange in the A-state. These have been identified through pH-jump experiments, which label them in the spectrum of the native protein. They were found to occur mainly in segments that are helical in the native structure. These results enable a model of the A-state to be proposed in which significant conformational freedom exists but where specific elements of native-like structure are preserved.

Animals↗
PubMed1989

A magnetization-transfer nuclear magnetic resonance study of the folding of staphylococcal nuclease.

The equilibrium between alternative folded states of a globular protein, staphylococcal nuclease, has been investigated by using 1H NMR. Magnetization-transfer experiments have revealed the existence of a related structural heterogeneity of the unfolded state, and quantitative analysis of a series of these experiments has permitted the kinetics of folding and interconversion of the different states to be explored. A model based on cis/trans isomerism at the peptide bond preceding Pro-117 has been developed to account for the results. This model, recently supported by a protein-engineering experiment [Evans et al. (1987) Nature (London) 329, 266], has been used to interpret the kinetic data, providing insight into the nature of the folding processes. The predominance of the cis-proline form in the folded state is shown to derive from a large favorable enthalpy term resulting from more effective overall folding interactions. The kinetics of folding and isomerization are shown to occur on similar time scales, such that more than one pathway between two states may be significant. It has been possible, however, to compare the direct folding and unfolding rates within the cis- and trans-proline-containing populations, with results suggesting that the specific stabilization of the cis peptide bond is effective only at a late stage in the folding process.

Isomerism↗
PubMed1989

A molecular dynamics analysis of protein structural elements.

The relation between protein secondary structure and internal motions was examined by using molecular dynamics to calculate positional fluctuations of individual helix, beta-sheet, and loop structural elements in free and substrate-bound hen egg-white lysozyme. The time development of the fluctuations revealed a general correspondence between structure and dynamics; the fluctuations of the helices and beta-sheets converged within the 101 psec period of the simulation and were lower than average in magnitude, while the fluctuations of the loop regions were not converged and were mostly larger than average in magnitude. Notable exceptions to this pattern occurred in the substrate-bound simulation. A loop region (residues 101-107) of the active site cleft had significantly reduced motion due to interactions with the substrate. Moreover, part of a loop and a 3(10) helix (residues of 67-88) not in contact with the substrate showed a marked increase in fluctuations. That these differences in dynamics of free and substrate-bound lysozyme did not result simply from sampling errors was established by an analysis of the variations in the fluctuations of the two halves of the 101 psec simulation of free lysozyme. Concerted transitions of four to five mainchain phi and psi angles between dihedral wells were shown to be responsible for large coordinate shifts in the loops. These transitions displaced six or fewer residues and took place either abruptly, in 1 psec or less, or with a diffusive character over 5-10 psec. Displacements of rigid secondary structures involved longer timescale motions in bound lysozyme; a 0.5 A rms change in the position of a helix occurred over the 55 psec simulation period. This helix reorientation within the protein appears to be a response to substrate binding. There was little correlation between the solvent accessible surface area and the dynamics of the different structural elements.

Binding Sites↗
PubMed1988

Sequential 1H NMR assignments and secondary structure of hen egg white lysozyme in solution.

Assignments for 1H NMR resonances of 121 of the 129 residues of hen egg white lysozyme have been obtained by sequence-specific methods. Spin systems were identified with phase-sensitive two-dimensional (2-D) correlated spectroscopy and single and double relayed coherence transfer spectroscopy. For key types of amino acid residues, particularly alanine, threonine, valine, and glycine, complete spin systems were identified. For other residues a less complete definition of the spin system was found to be adequate for the purpose of sequential assignment. Sequence-specific assignments were achieved by phase-sensitive 2-D nuclear Overhauser enhancement spectroscopy (NOESY). Exploitation of the wide range of hydrogen exchange rates found in lysozyme was a useful approach to overcoming the problem of spectral overlap. The sequential assignment was built up from 21 peptide segments ranging in length from 2 to 13 residues. The NOESY spectra were also used to provide information about the secondary structure of the protein in solution. Three helical regions and two regions of beta-sheet were identified from the NOESY data; these regions are identical with those found in the X-ray structure of hen lysozyme. Slowly exchanging amides are generally correlated with hydrogen bonding identified in the X-ray structure; a number of exceptions to this general trend were, however, found. The results presented in this paper indicate that highly detailed information can be obtained from 2-D NMR spectra of a protein that is significantly larger than those studied previously.

Amino Acid Sequence↗
PubMed1988

Paraffin section immunophenotyping of non-Hodgkin's lymphoma, using a panel of monoclonal antibodies.

The monoclonal antibodies F8-11-13, 4KB5, MB1, and MB2 recognize largely B-cell-restricted antigenic determinants that resist routine processing. Similarly, MT1, MT2, and UCHL1 react with fixation-resistant T-cell-restricted antigens. In order to evaluate the diagnostic potential of these antibodies, the authors have assessed their immunoreactivity with a series of 81 formalin-fixed and paraffin-embedded non-Hodgkin's lymphomas (48 B-cell, 33 T-cell) encompassing a wide variety of histologic subtypes, which had been fully characterized by frozen-section immunophenotyping. Ninety-six percent of B-cell lymphomas reacted with one or more of the B-cell-associated antibodies, whereas 100% of T-cell lymphomas reacted either with MT1, UCHL1, or both antibodies. MT2 was of no value in distinguishing between B- and T-cell lymphomas. None of the antibodies was entirely lineage specific; furthermore, a proportion of cases failed to react with one or more of the B- or T-cell-associated antibodies. Although these antibodies provide useful information in distinguishing between T- and B-cell lymphomas, the authors suggest that a panel of these antibodies is necessary for accurate determination of the histogenesis of these tumors. As with any immunohistochemical marker, interpretation of the immunostaining must be in the context of the morphologic features.

Antibodies, Monoclonal↗
PubMed1987

A 31P MAS NMR study of cytidine 2'-phosphate bound to ribonuclease A in the crystalline state.

31P CP/MAS spectra have been obtained from 2'-CMP bound to ribonuclease A in the crystalline state. The chemical shift value is closely similar to that found in solution NMR studies under similar conditions, and corresponds to that of the dianionic state of the free compound. It is suggested that the NMR approach may be of general applicability for the comparison of the binding properties of small molecules to proteins in crystals and solution.

Binding Sites↗
PubMed1987

Electrostatic effects and hydrogen exchange behaviour in proteins. The pH dependence of exchange rates in lysozyme.

The pH dependence of the exchange rates for a number of tryptophan and amide hydrogen atoms in hen egg-white lysozyme has been determined at temperatures well below the thermal denaturation temperature. The pH behaviour of each hydrogen is unique and can differ markedly from that of simple compounds. A model for electrostatic effects in proteins is described and used to explain a number of the features of the pH dependence of the exchange rates of certain hydrogens. The results indicate that exchange takes place from a conformation of the protein closely similar to that of the native protein, with local fluctuations providing the mechanism for exchange. For the more-buried hydrogens at low pH values there is a general increase in the exchange rates caused by the decreasing stability of the protein as calculated from the electrostatic model. The analysis shows how evidence from hydrogen exchange studies can be used to provide information about electrostatic interactions in localized regions of proteins. A description of the electrostatic model and some applications are given in the Appendix.

Amino Acid Sequence↗
PubMed1987

Conformations of intermediates in the folding of the pancreatic trypsin inhibitor.

Intermediates in the folding pathway of the bovine pancreatic trypsin inhibitor (PTI) have been examined by 1H nuclear magnetic resonance (n.m.r.). The intermediates were trapped during the reoxidation and consequent refolding of reduced PTI by alkylating free thiols; each intermediate contained different disulphide linkages. The n.m.r. spectra reveal that conformational features of the native protein are present in the intermediate containing just one of the three normal disulphide linkages (30-51). As additional normal disulphide bonds are formed, the conformation becomes more similar to that of the native protein. Introduction of additional but incorrect disulphide bonds does not lead to an increase in observable globular structure. A description of the folding process in terms of the conformations of the different intermediates is proposed. The significance of these results for the general mechanism of protein folding is outlined.

Amino Acid Sequence↗
PubMed1987

Immunohistochemical staining of non-Hodgkin's lymphoma in paraffin sections using the MB1 and MT1 monoclonal antibodies.

We have performed a single blind trial to assess the value of the monoclonal antibodies MB1 and MT1 in lymphoma classification. Sixty cases of non-Hodgkin's lymphoma (NHL) were stained with MB1 and MT1 using an indirect immunoperoxidase technique in paraffin sections. The majority of B tumours (27/33) stained with MB1, and most of the T tumours (24/27) stained with MT1. The MB1 antibody often produced rather weak staining but it was apparently highly specific for B cells, with only three (3/27) of the T tumours (two cases of 'malignant histiocytosis' of the intestine (MHI) and one pleomorphic T-cell lymphoma) displaying 'false' positivity. The MT1 antibody generally produced very strong staining, but it was not very selective, with 14/33 of the B lymphomas displaying 'false' positivity. the cross-reactivity observed in 17 cases led to only three misdiagnoses, two B tumours being designated as T lymphomas and one T tumour being designated as a B lymphoma. In a few cases (7/17), dual staining with both antibodies precluded firm diagnosis. In other cases (6/17), classification was possible despite some of the tumour cells showing dual staining. The seventeenth case was a plasmacytoma displaying MT1 positivity only. While the monoclonal antibodies MB1 and MT1 are of use in classifying lymphomas in paraffin section, they are not entirely lineage-specific, and the uncritical use of these two reagents alone may give rise to misdiagnosis; the use of a panel of monoclonal antibodies may yield more accurate results. As with any immunohistochemical marker, their limitations should be recognized; interpretation must be judicious and always in the context of the histological appearances.

Antibodies, Monoclonal↗
PubMed1987

Polycystic disease of the parotid glands: case report of a rare entity and review of the literature.

We report a case of polycystic disease of the parotid glands. This is a rare disorder and we know of only two previous documented cases in the literature. The disease presents with painless enlargement of one or both parotid glands and is not associated with any clinical abnormality of salivation or with any apparent anomaly of the other salivary glands. Histologically, the overall glandular architecture is preserved but the lobules are all markedly distended by epithelial-lined cysts, which appear to be derived from the intercalated ducts. Characteristic congophilic laminated spheroliths are present within the cystic spaces. The condition must be differentiated from cystic neoplasms, particularly papillary cystic adenocarcinoma, and from various non-neoplastic disorders including sialectasia, retention cysts and lymphoepithelial cysts.

Adult↗
PubMed1986

Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations.

Molecular dynamics simulations of hen egg-white lysozyme in the free and substrate-bound states are reported and the nature of the average structures and atomic fluctuations are analyzed. Crystallographic water molecules of structural importance, as determined by hydrogen-bonding, were included in the simulations. Comparisons are made between the dynamics and the X-ray results for the atomic positions, the main-chain and side-chain dihedral angles, and the hydrogen-bonding geometry. Improvements over earlier simulations in the potential energy function and methodology resulted in stable trajectories with the C alpha co-ordinates within 1.5 A of the starting X-ray structure. Structural features analyzed in the simulations agreed well with the X-ray results except for some surface residues. The Asx chi 2 dihedral distribution and the geometry of hydrogen bonding at reverse turns show differences; possible causes are discussed. The relation between the magnitudes and time-scales of the residue fluctuations and secondary structural features, such as helices beta-sheets and coiled loops, is examined. Significant differences in the residue mobilities between the simulations of the free and substrate-bound states were found in a region of the enzyme that is in direct contact with the substrate and in a region that is distant from the active-site cleft. The dynamic behavior of the structural water molecules is analyzed by examining the correlation between the fluctuations of the water oxygens and the lysozyme heavy-atoms to which they are hydrogen-bonded.

Animals↗
PubMed1985

Assignment of resonances in the 1H NMR spectrum of human lysozyme.

Assignments in the 1H NMR spectrum for more than 120 resonances arising from 38 of the 130 amino acid residues of human lysozyme are presented. Assignments have been achieved using a combination of one and two-dimensional NMR techniques. Two-dimensional double-quantum correlated spectroscopy and relayed coherence transfer spectroscopy were found to be particularly useful for the identification of spin systems in the aromatic and methyl regions of the spectrum. These spin systems were assigned to specific residues in human lysozyme with reference to the X-ray crystal structure using one-dimensional nuclear Overhauser enhancement (NOE) data and a computer-based search procedure. Unique assignments were found for resonances of 27 amino acid residues even when a distance constraint on NOE effects of 0.7 nm was used in the search procedure; for the remaining residues closer constraints or additional information were required. The assignments include all but one of the resonances in the aromatic region of the spectrum and all the methyl group resonances in the region upfield of 0.6 ppm. The assignments presented here provide a basis for a comparison of the NMR spectra of human lysozyme and the more widely studied hen lysozyme.

Amino Acids↗