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Biomedical subjects

S J Perkins

Publications and source records attributed to S J Perkins.

At least 109 records · Page 6Linked to original sources
PubMed1985

Molecular modelling of human complement subcomponent C1q and its complex with C1r2C1s2 derived from neutron-scattering curves and hydrodynamic properties.

Models for the structures of subcomponent C1q of first component C1 of human complement and its complex with subunit C1r2C1s2 are compared with experimental neutron-scattering curves. The length of the C1q collagenous arm is closer to 14.5 nm than to 11.5 nm proposed from electron microscopy, and this is consistent with the primary sequence of C1q. The mean C1q base-arm angle is 40-45 degrees and C1q is found to be flexible: the base-arm angle can vary up to 30 degrees from equilibrium at any moment. The complex of C1r2C1s2 and C1q requires a large shape change in C1r2C1s2. Ring-like models for C1r2C1s2 are not as successful at rationalizing the scattering data as are models that involve C1r2C1s2 binding to one side of C1q. Hydrodynamic calculations of the sedimentation coefficients for C1q and C1 are generally consistent with these neutron models.

Complement Activating Enzymes↗
PubMed1985

The shapes of biantennary and tri/tetraantennary alpha 1 acid glycoprotein by small-angle neutron and X-ray scattering.

Two forms of alpha 1 acid glycoprotein (orosomucoid) have been studied using small-angle neutron and X-ray scattering techniques; in one form all the five glycan chains were biantennary, while in the other they were either triantennary or tetraantennary. The radius of gyration RG was found to be sensitive to salt for the biantennary form, but to be unchanged up to an ionic strength of 3 M for the triantennary and tetraantennary forms. Conformational heterogeneity is thus associated with carbohydrate heterogeneity. Hydrodynamic frictional coefficients confirm these findings. Simple models of alpha 1 acid glycoprotein were developed to account for the RG and values. These show that the compact conformation is slightly more elongated than a globular protein and that the expanded biantennary conformation has a most extended carbohydrate structure. Up to half of the surface of the compact shape can be covered by carbohydrate residues.

Amino Acids↗
PubMed1984

Neutron scattering studies of subcomponent C1q of first component C1 of human complement and its association with subunit C1r2C1s2 within C1.

Neutron scattering studies are reported on subcomponent C1q of component C1 of human complement, and on C1, the complex of C1q with subunit C1r2C1s2. For C1q, the molecular weight was determined as 460,000. The radius of gyration at infinite contrast RC is 12.8 nm. The RC values for the proteolytically cleaved forms of C1q, namely the heads and the stalks, are 1.5 to 2 nm and 11 nm, respectively, and thus the axis-to-arm angle of C1q is estimated at 45 degrees. Neutron data for subunit C1r2C1s2 are published elsewhere. The neutron data on C1 lead to an RC value of 12.6 nm for proenzymic C1 and a molecular weight of 820,000. The wide-angle scattering curve of C1q exhibits a minimum at Q = 0.28 nm-1 and a maximum at 0.39 nm-1; on the addition of C1r2C1s2, this minimum disappears. The neutron data on C1 indicate that C1q and C1r2C1s2 have complexed with a large conformational change in one or both parts. No conformational changes can be detected on the activation of C1 by this method.

Complement Activating Enzymes↗
PubMed1983

Low-resolution structural studies of mitochondrial ubiquinol:cytochrome c reductase in detergent solutions by neutron scattering.

Mitochondrial ubiquinol:cytochrome c reductase (Mr approximately 600,000) was cleaved into a complex (Mr approximately 280,000) of the subunits III (cytochrome b), IV (cytochrome c1) and VI to IX, a complex (Mr approximately 300,000) of the subunits I and II, and the single subunit V (iron-sulphur subunit, Mr approximately 25,000). Neutron scattering was applied to the whole enzyme, the cytochrome bc1 complex, both in hydrogenated and deuterated alkyl (phenyl) polyoxyethylene detergents, and the complex of subunits I and II in detergent-free solution. The neutron parameters were compared with the structures of the enzyme and the cytochrome bc1 complex previously determined by electron microscopy. Using the method of hard spheres, comparison of the calculated and experimental radius of gyration implies that the length of the enzyme across the bilayer or the detergent micelle is between 150 and 175 A and of the cytochrome bc1 complex between 90 and 115 A. The subunit topography was confirmed. The cleavage plane between the cytochrome bc1 complex and the complex of subunits I and II lies at the centre of the enzyme and runs parallel to the membrane just outside the bilayer. The detergent uniformly surrounds the protein as a belt, which is displaced by 30 to 40 A from the protein centre of the enzyme and by about 20 A from the protein centre of the cytochrome bc1 complex. The low protein matchpoint of the whole enzyme as compared to the subunit complexes is accounted for in terms of the non-exchange of about 30 to 60% of the exchangeable protons within the intact enzyme. Polar residues are, on average, at the protein surface and non-polar residues and polar residues with non-exchanged protons are buried within the enzyme.

Amino Acids↗
PubMed1983

alpha 1 acid glycoprotein: a small-angle neutron scattering study of a human plasma glycoprotein.

Small-angle neutron scattering experiments on alpha 1 acid glycoprotein showed that it has a molecular weight of 37000 and a matchpoint of 44.7% 2H2O. The molecular weight, the matchpoint and a v of 0.704 ml/g are in agreement with the primary sequence and standard residue volumes for amino acids and carbohydrates. The radius of gyration RG of alpha 1 acid glycoprotein was found to be independent of concentration in the range 2-11 mg/ml, but increases on going from a buffer containing 0.2 M NaCl to one containing 1 M NaCl. A contrast variation study showed that the RG at infinite contrast is 2.47 nm for the expanded form and 2.19 nm for the contracted form, and that the two Stuhrmann alpha values are similar at 27 X 10(-5). The latter is greater than that expected for globular proteins and are explained by the surface disposition of the five glycan chains on a core of protein in alpha 1 acid glycoprotein. Modelling calculations account for the two RG values in which for the expanded form the glycan chains extend out into the solvent and for the contracted form they either fold back or are splayed out such that they are able to interact with the surface of the protein core.

Carbohydrate Conformation↗
PubMed1983

Neutron scattering studies of the isolated C1r2C1s2 subunit of first component of human complement in solution.

The subunit complex C1r2C1s2 of the first component of complement was investigated by small-angle neutron scattering in both the activated and unactivated forms. From these experiments, a molecular weight of 390,000 for C1r2C1s2 was found. The matchpoint was determined to be 43% 2H2O. Both results are consistent with composition data. The partial specific volume is 0.751 ml/mg. The radius of gyration at infinite contrast was found to be 17 nm for C1r2C1s2 and 1.1 nm for the cross section. Models for C1r2C1s2 were computed by the method of hard spheres, in which C1r2C1s2 was represented by spheres 0.87 nm diameter arranged in a straight rod of length 59 nm and a circular cross section of 3.2 nm. This rod can be bent at one or two places by up to 60 degrees without significant effect on the calculated radii of gyration. The model is in agreement with published ultracentrifugation and electron microscopy data.

Amino Acids↗
PubMed1981

Estimation of deuteration levels in whole cells and cellular proteins by 1H n.m.r. spectroscopy and neutron scattering.

Methods using conventional Fourier transform 1H n.m.r. spectroscopy at 250 MHz for the determination of the overall deuteration levels of cells cultured in media containing 2H2O or deuterated carbon sources are described. These were developed for Escherichia coli as a model, and extended to Neurospora crassa hyphae and mouse myeloma cells P815. The results were investigated by 1H n.m.r. and neutron scattering measurements on deuterated proteins that were obtained from E. coli. It is concluded that 1H n.m.r. is able to observe the soluble proteins of E. coli in certain cases, that deuteration levels can be determined by 1H n.m.r. for small quantities of proteins in their native state, and that glycerol is a more efficient carbon source than glucose for the deuteration of E. coli proteins.

Animals↗
PubMed1981

The binding of monosaccharide inhibitors to hen egg-white lysozyme by proton magnetic resonance at 270 MHz and analysis by ring-current calculations.

Studies of the binding of the four sugars alpha- and beta-N-acetyl-D-glucosamine (GlcNAc) and its alpha- and beta-methyl glycosides to hen egg-white lysozyme (EC 3.2.1.17) by means of high-resolution 1H n.m.r. at 270 MHz are reported. The details of the binding analyses are described in an Appendix. The results show that the sugars bind independently to more than one site in lysozyme. The apparent fully bound chemical shifts to the inhibitor proton signals show that, although the major binding modes are generally similar for the four sugars, the binding of alpha GlcNAc is distinct from that of alpha MeGlcNAc and beta MeClcNAc. The binding of beta GlcNAc is intermediate in character between these two modes. The observed shift changes of the inhibitor signals are correlated with the crystal structures of lysozyme-inhibitor complexes by the use of Johnson-Bovey ring-current calculations. Together with consideration of the chemical-shift anisotropy of the GlcNAc amide group, these suggest that GlcNAc-binding sites in solution are in subsites C and E. The calculations show also that the indole rings of Trp-62 and Trp-63 rotate towards subsite C on the binding of GlcNAc, whereas Trp-108 moves away slightly. These findings indicate a difference between the solution and tetragonal crystal forms of lysozyme-GlcNAc and lysozymes-beta MeGlcNAc complexes. In the crystal structure, binding of acetamido monosaccharides is only observed in subsite C, and binding in subsite E is prevented by crystal packing.

Acetylglucosamine↗
PubMed1981

The simultaneous binding of lanthanide and N-acetylglucosamine inhibitors to hen egg-white lysozyme in solution by 1H and 13C nuclear magnetic resonance.

Lanthanide ions and the N-acetylglucosamine (GlcNAc) sugars are able to bind simultaneously to hen egg-white lysozyme (EC 3.2.1.17). The present study characterizes the properties of the ternary complexes with lysozyme, which involve up to seven paramagnetic lanthanides and two diamagnetic lanthanides, together with alpha GlcNAc, beta GlcNAc, alpha MeGlcNAc and beta MeGlcNAc. pH titrations and binding titrations of the GlcNAc sugars with lysozyme-La(III) complexes show that the GlcNAc sugars bind to at least two independent sites and that one of them competes with La(III) for binding to lysozyme. Given the known binding site of lanthanides at Asp-52 and Glu-35, the competitive binding site of GlcNAc is identified as subsite E. A simple analysis of the paramagnetic-lanthanide-induced shifts shows that the GlcNAc sugar binds in subsite C, in accordance with crystallographic results [Perkins, Johnson, Machin & Phillips (1979) Biochem. J. 181, 21-36]. This finding was refined by several computer analyses of the lanthanide-induced shifts of 17 proton and carbon resonances of beta MeGlcNAc. Good fits were obtained for all the signals, except for two that were affected by exchange broadening phenomena. No distinction could be made between a fit for a two-position model of Ln(III) binding with axial symmetry to lysozyme, according to the crystallographic result, or a one-position model with axial symmetry where the Ln(III) is positioned mid-way between Asp-52 and Glu-35. Although this work establishes the feasibility of lanthanide shift reagents for study of protein-ligand complexes, further work is required to establish the manner in which lanthanides bind to lysozyme in solution.

Acetylglucosamine↗
PubMed1980

Comparisons of ring-current shifts calculated from the crystal structure of egg white lysozyme of hen with the proton nuclear magnetic resonance spectrum of lysozyme in solution.

Detailed ring-current calculations with some consideration for protein flexibility are described for egg white lysozyme of hen. These are based on 15 sets of crystal coordinates of lysozyme and over 60 assigned resonances in the 1H nuclear magnetic resonance (NMR) spectrum of lysozyme. These analyses evaluate two basic assumptions: that the refined protein crystal structure is similar to the protein structure in solution and that the present ring-current theories in application to the aromatic amino acids offer a good description of the observed shifts in the protein NMR spectrum. The dipolar, Johnson-Bovey, and Haigh-Mallion equations are tested. The conventional ring-current intensity factors for the tyrosine and phenylalanine rings of 0.94 and 1.00 are found to be satisfactory, but those for the tryptophan ring need to be increased. With this, ring-current effects offer good explanations for the chemical shifts of the aliphatic and aromatic protons in lysozyme for which the NMR signals have to date been resolved and assigned. Ring-current effects do not, however, explain directly the shifts of the six tryptophan N-H protons nor those of the alpha protons. Applications of these calculations are described to compare the tetragonal and triclinic forms of native lysozyme, to propose several assignments of 1H NMR signals in the spectrum of lysozyme, and to analyze some of the conformational changes which occur on the binding of Gd(III) and GlcNAc sugars to lysozyme. The uses and limitations of the calculations for protein NMR are briefly discussed.

Computers↗
PubMed1979

Crystal structures of hen egg-white lysozyme complexes with gadolinium(III) and gadolinium(III)-N-acetyl-D-glucosamine.

Analysis at 0.25 nm resolution of the crystal structures of lysozyme-Gd(III) and lysozyme-Gd(III)-N-acetyl-D-glucosamine (GlcNac), prepared by diffusion methods, show that there are two main binding positions for Gd(III), one of which is close to glutamic acid-35 and the other close to aspartic acid-52. The two sites are 0.36 nm part. There is no evidence for the weak binding of Gd(III) to any of the eight other carboxy groups of lysozyme. In the presence of Gd(III), the binding of GlcNac is similar to that observed for the binding of the beta-anomer in subsite C. There are numerous small conformational changes in the protein on binding (Gd(III) and the sugar, and these have been quantified to a first approximation by real-space refinement. These changes are similar in both structures, and involve, among other small movements, shifts of one of the disulphide bridges by up to 0.05 nm. The movement of residues 70--74 observed in the binary complex of lysozyme-GlcNac [Perkins, Johnson, Machin & Phillips (1978) Biochem. J. 173-617] is not observed in the ternary complex of lysozyme-Gd(III)-GlcNac. The nature of the lysozyme-Gd(III) complex is discussed in the light of evidence from other crystallographic studies and n.m.r. solution studies. Preliminary findings for a lysozyme-Gd(III) complex prepared by co-crystallization methods are reported.

Acetylglucosamine↗
PubMed1979

Ring current effects in the conformation dependent NMR chemical shifts of aliphatic protons in the basic pancreatic trypsin inhibitor.

Previously, a highly refined crystal structure and energy refined atomic coordinates were obtained for the basic pancreatic trypsin inhibitor, as well as numerous individual resonance assignments in the 1H NMR spectrum. These data were now used to investigate the contributions from the local ring current fields of the aromatic rings to the overall conformation dependent chemical shifts in this globular protein. A program was written which allowed the consideration of certain aspects of internal mobility of the protein, and the different commonly used ring current equa tions were compared. These studies indicate that ring current shifts are the dominant contribution to the observed conformation dependent chemical shifts of the peripheral aliphatic side chain protons. On the other hand, it appears that ring current shifts do not make dominant contributions to the conformation dependent shifts of the backbone alpha- and amide protons or the aromatic protons in the inhibitor. On the basis of the empirical calibration with the peripheral aliphatic side chain protons, the Johnson-Bovey ring current equation was selected for an analysis of the ring geometries of two prolines in the inhibitor.

Amino Acids↗
PubMed1978

Structural interpretation of lanthanide binding to the basic pancreatic trypsin inhibitor by 1H NMR at 360 MHz.

The weak binding of lanthanides to the five carboxyl groups of the basic pancreatic trypsin inhibitor (hereafter termed "the inhibitor"), has been investigated in detail using high resolution 1H NMR at 360 MHz. Lanthanides bind to the C-terminus with an apparent binding constant of 30 M-1, and thus competitively inhibit the formation of a salt-bridge between the C-terminus and the N-terminus, Lanthanides bind also to the side chain carboxyl groups of Asp 3, Glu 7, Glu 49 and Asp 50, with binding constants of 10--30 M-1. With the use of lanthanides individual resonance assignments for Phe 4 and Phe 45 were obtained in the 1H NMR spectrum of the inhibitor, and for several spin systems previous identifications were independently confirmed. The present experiments also provide a nice illustration for the use of shift reagents to improve the resolution in 1H NMR spectra of proteins. The exchange broadening for Tyr 35 and Phe 45 over the temperature range 4--72 degrees C could thus be observed for almost all the components of these aromatic spin systems and new details on the dynamic properties were obtained also for other aromatic residues.

Amino Acid Sequence↗