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Biomedical subjects

H M Baker

Publications and source records attributed to H M Baker.

At least 37 records · Page 2Linked to original sources
PubMed1998

Structural basis of the Tanford transition of bovine beta-lactoglobulin.

The structures of the trigonal crystal form of bovine beta-lactoglobulin variant A at pH 6.2, 7.1, and 8.2 have been determined by X-ray diffraction methods at a resolution of 2.56, 2. 24, and 2.49 A, respectively. The corresponding values for R (Rfree) are 0.192 (0.240), 0.234 (0.279), and 0.232 (0.277). The C and N termini as well as two disulfide bonds are clearly defined in these models. The glutamate side chain of residue 89 is buried at pH 6.2 and becomes exposed at pH 7.1 and 8.2. This conformational change, involving the loop 85-90, provides a structural basis for a variety of pH-dependent chemical, physical, and spectroscopic phenomena, collectively known as the Tanford transition.

Animals↗
PubMed1998

Crystal structure of a human embryonic haemoglobin: the carbonmonoxy form of gower II (alpha2 epsilon2) haemoglobin at 2.9 A resolution.

The production of recombinant embryonic haemoglobins via a yeast expression system has enabled structural and functional studies to be conducted on these proteins. As part of a programme aimed at understanding the properties of the embryonic haemoglobins we have crystallized the human alpha2 epsilon2 (Gower II) embryonic haemoglobin in its carbonmonoxy form, and determined its structure by X-ray crystallography. The structure was solved by molecular replacement and refined at 2.9 A to give a final model with R-factor=0.185 and Rfree=0.235. The Gower II hemoglobin tetramer is intermediate between the adult R and R2 states, though closer to R2. The tertiary structure of the conserved alpha subunit is essentially identical when compared to that found in the adult (alpha2 beta2) and fetal (alpha2 gamma2) hemoglobins. The embryonic epsilon subunit has a structure very similar to that of the homologous adult beta and fetal gamma subunits, although with small differences at the N terminus and in the A helix. Amino acid substitutions can be identified that may play a role in the altered response of the Gower II haemoglobin to allosteric effectors, in particular chloride ions. The reduced chloride effect is thought to be the primary cause of the higher affinity of this embryonic hemoglobin in comparison to the adult molecule.

Heme↗
PubMed1997

Crystal structure of the streptococcal superantigen SPE-C: dimerization and zinc binding suggest a novel mode of interaction with MHC class II molecules.

Bacterial superantigens are small proteins that have a very potent stimulatory effect on T lymphocytes through their ability to bind to both MHC class II molecules and T-cell receptors. We have determined the three-dimensional structure of a Streptococcal superantigen, SPE-C, at 2.4 A resolution. The structure shows that SPE-C has the usual superantigen fold, but that the surface that forms a generic, low-affinity MHC-binding site in other superantigens is here used to create a SPE-C dimer. Instead, MHC class II binding occurs through a zinc binding site that is analogous to a similar site in staphylococcal enterotoxin A. Consideration of the SPE-C dimer suggests a novel mechanism for promotion of MHC aggregation and T-cell activation.

Amino Acid Sequence↗
PubMed1997

Rules outside the rules for administration of medication: a study in New South Wales, Australia.

PURPOSE: To improve understanding of how nurses define or redefine medication error. DESIGN: Qualitative descriptive. METHODS: This 18-week ethnomethodological study in one hospital used participant observation, documentary analysis, and validation criteria. Ethnomethodology is useful for making clearer the every-day, taken-for-granted understandings and practices of people as they make sense of their world. It hinges on the use of tacitly held knowledge in practical situations. FINDINGS: Nurses adopted practices and embodied logic to accomplish tasks. They created criteria to decide when incidents were "real errors" and used institutional rules to create order. CONCLUSIONS: The findings provide a body of tacitly held knowledge about medication error that is shared among clinical nurses and redefines medication error using six criteria. The study calls into question the way institutions seek to identify, document, and reduce medication errors by nurses and the validity of nursing research based on reported error rates.

Humans↗
PubMed1996

Anion binding by transferrins: importance of second-shell effects revealed by the crystal structure of oxalate-substituted diferric lactoferrin.

Proteins of the transferrin family bind, with high affinity, two Fe3+ ions and two CO3(2)- ions but can also bind other metal ions and other anions. In order to find out how the protein structure and its two binding sites adapt to the binding of larger anions, we have determined the crystal structure of oxalate-substituted diferric lactoferrin at 2.4 A resolution. The final model has a crystallographic R-factor of 0.196 for all data in the range 8.0-2.4 A. Substitution of oxalate for carbonate does not produce any significant change in the polypeptide folding or domain closure. Both binding sites are perturbed, however, and the effects are different in each. In the C-lobe site the oxalate ion is bound to iron in symmetric 1,2-bidentate fashion whereas in the N-lobe the anion coordination is markedly asymmetric. The difference arises because in each site substitution of the larger anion causes displacement of the arginine that forms one wall of the anion binding site; the movement is different in each case, however, because of different interactions with "second shell" amino acid residues in the binding cleft. These observations provide an explanation for the site inequivalences that accompany the substitution of non-native anions and cations.

Anions↗
PubMed1996

Crystallization and preliminary X-ray diffraction studies of a cobalt-substituted derivative of the iron-dependent alcohol dehydrogenase from Zymomonas mobilis.

The iron-dependent alcohol dehydrogenase from Zymomonas mobilis has been crystallized in a form suitable for X-ray diffraction studies. The crystals grew in hanging drops by vapor diffusion, equilibrating with a solution comprising 25-27% methoxypolyethylene glycol 5000 and 1 mM Co(2+) in a 0.2 M succinic acid/potassium hydroxide buffer at pH 5.5-5.7 at 281 K. Crystals are tetragonal, P4(1)22 (or P4(3)22), with unit-cell dimensions a = b = 125.7, c = 248.1 A. Four molecules comprise the asymmetric unit, and a self-rotation function indicates twofold local symmetry perpendicular to the unique axis and 15 degrees from a crystallographic twofold axis. Diffraction data to 3.0 A have been collected.

Journal Article↗
PubMed1995

1.8 A crystal structure of the C-terminal domain of rabbit serum haemopexin.

BACKGROUND: Haemopexin is a serum glycoprotein that binds haem reversibly and delivers it to the liver where it is taken up by receptor-mediated endocytosis. Haemopexin has two homologous domains, each having a characteristic fourfold internal sequence repeat. Haemopexin-type domains are also found in other proteins, including the serum adhesion protein vitronectin and various collagenases, in which they mediate protein-protein interactions. RESULTS: We have determined the crystal structure of the C-terminal domain of haemopexin at 1.8 A resolution. The domain is folded into four beta-leaflet modules, arranged in succession around a central pseudo-fourfold axis. A funnel-shaped tunnel through the centre of this disc-shaped domain serves as an ion-binding site. CONCLUSIONS: A model for haem binding by haemopexin is proposed, utilizing an anion-binding site at the wider end of the central tunnel, together with an associated cleft. This parallels the active-site location in other beta-propeller structures. The capacity to bind both cations and anions, together with the disc shape of the domain, suggests that such domains may be used widely for macromolecular recognition.

Amino Acid Sequence↗
PubMed1995

Secretion of atrial natriuretic peptide and vasopressin by small cell lung cancer.

BACKGROUND: Hyponatremia in patients with small cell lung cancer (SCLC) is a common clinical problem usually attributed to tumor secretion of arginine vasopressin (AVP). It recently was shown that some SCLC cell lines produce atrial natriuretic peptide (ANP). The purpose of this investigation was to determine the frequency and clinical consequences of secretion of ANP by SCLC and the relative contribution of ANP and AVP to the hyponatremia associated with this disease. METHODS: Levels of ANP and AVP were measured in 23 SCLC cell lines and 23 other human tumor cell lines. Also, ANP and AVP levels were determined in plasma samples from 69 patients with active small cell carcinomas. RESULTS: Of the 23 SCLC lines, 16 (70%) had elevated ANP levels. Only two (8.7%) had elevated AVP levels, and these two also had elevated ANP levels. One of the ANP-producing cell lines was derived from a hyponatremic patient with no other apparent explanation for a low sodium level. However, the four cell lines with the highest levels of ANP were derived from patients who were not hyponatremic. Two other human tumor lines also produced ANP. Of the 69 patients with SCLC, 21 (30.4%) had elevated ANP levels, whereas 4 (6%) had elevated AVP levels. Fifteen of these patients were hyponatremic during their clinical course (21.7%). Of the eight patients who were hyponatremic when samples were collected, two had elevated ANP levels, and only one had elevated AVP levels. Six patients (8.7%) had symptoms of postural hypotension, possibly attributable in some cases of tumor secretion of ANP. CONCLUSIONS: The majority of SCLC lines produce ANP, and a minority produce AVP. Secretion of ANP may result in hyponatremia and/or postural hypotension. However, secretion of either or both of these peptides does not account for all cases of hyponatremia in patients with SCLC and does not necessarily cause clinical manifestations.

Adenocarcinoma↗
PubMed1994

Crystallization and preliminary X-ray diffraction studies on cytosolic (class 1) aldehyde dehydrogenase from sheep liver.

The cytosolic (Class 1) aldehyde dehydrogenase (AlDH) from sheep liver has been crystallized in a form suitable for X-ray diffraction studies. The crystals, grown by vapour diffusion using 6.5 to 7.5% methoxypolyethylene glycol 5000 as precipitant, at pH 6.5, are orthorhombic with cell dimensions a = 80.7, b = 92.5, c = 151.6 A, space-group P2(1)2(1)2(1), and one dimer in the asymmetric unit. The crystals diffract to at least 2.8 A resolution. Although unmodified AlDH crystallized readily, a key factor in obtaining diffraction-quality crystals was the covalent attachment of an active site reporter group, provided by 3,4-dihydro-3-methyl-6-nitro-2H-1,3-benzoxazin-2-one.

Aldehyde Dehydrogenase↗
PubMed1994

Enzymatic deglycosylation as a tool for crystallization of mammalian binding proteins.

Enzymatic deglycosylation has been used in attempts to crystallize several glycoproteins with the aim of overcoming the problems resulting from heterogeneity and flexibility of the attached glycan chains. An endoglycosidase preparation from Flavobacterium meningosepticum, comprising the enzymes endo F and PNGase-F, was used in experiments on the mammalian binding proteins lactoferrin and haemopexin. Significant differences were found in the susceptibility of different proteins to deglycosylation. For human lactoferrin (Lf) and its recombinant N-terminal half-molecule (Lf(N)), deglycosylation was rapid and complete, and was essential for obtaining high-quality crystals of both apo-Lf and Lf(N); for bovine Lf, however, complete deglycosylation did not occur. Similarly, for rabbit haemopexin the carbohydrate chain on the C-terminal domain was easily removed, but the three chains on the N-terminal domain proved more resistant and their removal led to some fragmentation of the protein. Nevertheless, this approach provided the only means of crystallizing the C-terminal domain and is likely to be useful for other glycoproteins.

Journal Article↗
PubMed1994

Search designs for protein crystallization based on orthogonal arrays.

In protein crystallography, the initial experimental problem is the identification of physical and chemical conditions that will support nucleation and crystal growth. Ideally, experiments to search for such conditions would be based on a full-factorial structure, with variation in the temperature and solution composition. However, consideration of even a moderate number of possibilities for the composition of the system will result in factorial experiments which may be prohibitively large. In this paper it is proposed that search experiments for protein crystallization might be based on orthogonal arrays. These are subsets of full-factorial experiments which possess a great deal of symmetry, such that a uniform distribution of points throughout the experimental region is preserved. Such experiments have reasonable size, explore the proposed experimental region in a systematic fashion, and form a logical basis for a sequential approach to the search for crystallization conditions. Examples of such initial search experiments are given, and their application to some recent protein crystallization problems in this laboratory is described briefly. The relationship of this approach to other protein crystallization search procedures is also discussed.

Journal Article↗
PubMed1994

Structure of copper- and oxalate-substituted human lactoferrin at 2.0 A resolution.

The three-dimensional structure of human dicupric monooxalate lactoferrin, Cu(2)oxLf, has been determined to 2.0 A resolution, using X-ray diffraction data collected by diffractometry to 2.5 A resolution, and oscillation photography on a synchrotron source to 2.0 A resolution. Difference electron-density maps calculated between Cu(2)oxLf and both dicupric lactoferrin, Cu(2)Lf, and diferric lactoferrin, Fe(2)Lf, showed that the oxalate had replaced a carbonate in the C-terminal binding site, and that, relative to Cu(2)Lf, there were no significant differences in the N-terminal site. The structure was then refined crystallographically by restrained least-squares methods. The final model, in which the r.m.s. deviation in bond distances is 0.017 A, contains 5314 protein atoms (691 residues), two Cu(2+) ions, one bicarbonate ion, one oxalate ion, 325 solvent molecules and one sugar residue. The crystallographic R factor of 0.193 is for 46 134 reflections in the range 8.0 to 2.0 A resolution. The oxalate ion is coordinated to copper in a 1,2-bidentate fashion, and the added bulk of the anion results in the rearrangement of the side chains of nearby arginine and tyrosine residues. No other major alterations in the molecule can be observed, the overall protein structure being the same as that for Cu(2)Lf and Fe(2)Lf.

Journal Article↗
PubMed1994

Three-dimensional structure of lactoferrin in various functional states.

The three-dimensional structures of various forms of lactoferrin, determined by high resolution crystallographic studies, have been compared in order to determine the relationship between structure and biological function. These comparisons include human apo and diferric lactoferrins, metal and anion substituted lactoferrins, the N-terminal half molecule of human lactoferrin, and bovine diferric lactoferrin. The structures themselves define the nature and location of the iron binding sites and allow anti-bacterial and putative receptor-binding regions to be mapped on to the molecular surface. The structural comparisons show that small internal adjustments can allow the accommodation of different metals and anions without altering the overall molecular structure, whereas large-scale conformational changes are associated with metal binding and release, and smaller, but significant, movements accompany species variations. The results also focus on differences in flexibility between the two lobes, and on the importance of interactions in the inter-lobe region in modulating iron release from the N-lobe and in possibly enabling binding at one site to be signalled to the other.

Animals↗
PubMed1994

Synergism and substitution in the lactoferrins.

The anion binding properties of human lactoferrin (Lf), with Fe3+ or Cu2+ as the associated metal ion, highlight differences between the two sites, and in the anion binding behaviour when different metals are bound. Carbonate, oxalate and hybrid carbonate-oxalate complexes have been prepared and their characteristic electronic and EPR spectra recorded. Oxalate can displace carbonate from either one or both anion sites of Cu2(CO3)2Lf, depending on the oxalate concentration, but no such displacement occurs for Fe2(CO3)2Lf although it does for the bovine analogue. Addition of oxalate and the appropriate metal ion to apoLf under carbonate-free conditions gives dioxalate complexes with both Fe3+ and Cu2+. The anion sites as determined from the crystal structures of Fe2(CO3)2Lf, Fe2(C2O4)2Lf, Cu2(CO3)2Lf, and Cu2(CO3)(C2O4)Lf have been compared. Both the carbonate and oxalate ions bind in bidentate fashion to the metal, except that the carbonate ion in the N-lobe site of dicupric lactoferrin is monodentate. The hybrid copper lactoferrin complex shows that the oxalate ion binds preferentially in the C-lobe site in a bidentate mode. A series of complexes containing the synergistic anion O,N-chelates with increasing substitution on the N atom (glycinate, iminodiacetate and nitrilotriacetate) have been prepared with iron bovine lactoferrin for comparison with the O,O-chelate oxalate. Overall these observations lead to a generalised model for synergistic anion binding by transferrins and allow comparisons to be made with nonsynergistic anions such as citrate and succinate.

Animals↗