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K D Gibson

Publications and source records attributed to K D Gibson.

At least 37 records · Page 2Linked to original sources
PubMed1991

Conformational energy studies of beta-sheets of model silk fibroin peptides. I. Sheets of poly(Ala-Gly) chains.

A new model structure is proposed for the silk I form of the crystalline domains of Bombyx mori silk fibroin and the corresponding crystal form of poly(L-Ala-Gly). It was deduced from conformational energy computations on stacked sheet structures of poly(L-Ala-Gly). The novel sheet structure contains interstrand hydrogen bonds but is composed of anti-parallel polypeptide chains whose conformation differs from that of the antiparallel beta-sheets that constitute the silk II structure. The strands of the new sheet have a two-residue repeat, in which the Ala residues adopt a right-handed and the Gly residues a left-handed sheet-like conformation. The computed unit cell is orthorhombic, with cell dimensions a = 8.94 A, b = 6.46 A, and c = 11.26 A. The model accounts for most spacings in the observed fiber x-ray diffraction patterns of silk I and of the silk-I-like form of poly(L-Ala-Gly), and it is consistent with nmr and ir spectroscopic data. As a test of the computations, the well-established beta-sheet structure of silk II and the corresponding form of poly(L-Ala-Gly) have been reproduced. The computed energies for the two forms of poly(L-Ala-Gly) indicate that the silk-II-like form is more stable, by about 1.0 kcal/mol per residue. The main difference between the two structures is the orientation of the Ala side chains of neighboring strands in each sheet. In the Pauling-Corey beta-sheet and in the silk II form, referred to as an "in-register" structure, the Ala side chains of every strand point to the same side of a sheet. In the silk I structure, referred to as "out-of-register," the side chains of Ala residues in adjacent strands point to opposite sides of the sheet.

Amino Acid Sequence↗
PubMed1990

Conformations of the central transforming region (Ile 55-Met 67) of the p21 protein and their relationship to activation of the protein.

The GTP-binding p21 protein, encoded by the ras-oncogene, becomes transforming if amino acid substitutions are made at critical positions in the polypeptide chain, e.g., at Gly 12, Gly 13, Ala 59, Gln 61 and Glu 63. Most of these substitutions occur in two phosphate-binding loop regions, Tyr 4-Thr 20, herein designated as segment 1, and Ile 55-Met 67, herein designated, as segment 2. These two segments are homologous to two corresponding regions in the two purine nucleotide binding proteins, bacterial elongation factor (EF-tu) (Val 12-Thr 28 corresponds to segment 1; His 78-Ile 92 corresponds to segment 2) and adenylate kinase (ADK) (Lys 9-Cys 25 corresponds to segment 1 and Tyr 95-Arg 107 corresponds to segment 2). We find that the conformations of the segment 1 region in the p21 protein, EF-tu and ADK are similar to one another and that the conformation of the segment 2 region of EF-tu is superimposable on that of segment 2 of ADK. Furthermore, the relative position of the two segments in EF-tu is strikingly similar to that of the two segments in ADK. In the originally proposed X-ray structure for the p21 protein, the conformation of segment 2 in the p21 protein is not similar to that found for the other two proteins, and its disposition relative to segment 1 and the remainder of the protein is also different from that observed for the other two proteins.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenylate Kinase↗
PubMed1989

A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. I. Conformational predictions for the tandemly repeated peptide (Asn-Ala-Asn-Pro)9.

A search for low-energy helical and near-helical conformations of the tandemly repeated peptide (Asn-Ala-Asn-Pro)9 was undertaken by minimization of the CHARMM potential energy function from eight starting conformations; the latter were obtained from the two low-energy conformations of this repeated peptide found by Gibson & Scheraga, Proc. Natl. Acad. Sci. USA 83, 5649-5653 (1986), and the single conformation found by Brooks et al., Proc. Natl. Acad. Sci. USA 84, 4470-4474 (1987), and from modifications of these three conformations. The same eight starting conformations, as determined by dihedral angles, were used for minimizations of the AMBER and ECEPP potentials. Comparison of the final conformations by least-squares superposition of their C alpha atoms, and by inspection of the parameters of the ideal helix or coiled coil that most closely matched the coordinates of their C alpha atoms in a least-squares sense, showed that: (1) energy minimization, starting from the same conformation but using any two different potentials, could lead to final conformations whose resemblance to each other varied from acceptable to highly unsatisfactory; (2) the ordering of the final energy-minimized conformations, and the energy differences between them, were quite different for all three potentials; (3) the extent of agreement or disagreement between pairs of conformations generated using CHARMM and AMBER, CHARMM and ECEPP, or AMBER and ECEPP, respectively, was not significantly different. The lowest-energy conformation generated using each of the potentials was a left-handed helix, whose pitch and number of residues per turn were similar to those of the left-handed helix found by Gibson & Scheraga. Although the starting conformation which led to the lowest-energy conformation was different for all three potentials, pairwise superposition of the C alpha atoms in the final conformations showed root-mean-square deviations of only 1.0-1.3 A. It is concluded that energy minimizations starting from a large enough sample of initial conformations might on occasion lead to essentially the same conformational prediction whichever potential is used; however, if the sample of starting points is small, predictions based on the three potentials will usually diverge.

Amino Acid Sequence↗
PubMed1989

A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests.

phi-psi maps of N-acetyl alanine N'-methyl amide have been computed using the CHARMM potential, the all-atom AMBER potential, and the ECEPP/2 potential, before and after adiabatic relaxation. Maps using the CHARMM and AMBER potentials were determined with values of 1.0 and 4.0 for the dielectric constant epsilon, and with a distance dependent dielectric constant. Adiabatic relaxation was carried out using flexible geometry for the CHARMM and AMBER potentials, and using rigid geometry for the AMBER and ECEPP potentials. In all cases, the lowest energy was found in the C7eq region (phi approximately -70 degrees, psi approximately 70 degrees). The maps with CHARMM and AMBER with epsilon = 4.0 and with ECEPP, without adiabatic relaxation, were broadly similar but differed in the relative energies allotted to high-energy regions of the map. After adiabatic relaxation with rigid geometry, the map with ECEPP, and the map with AMBER using a distance-dependent dielectric constant, agreed fairly well apart from differences in the relative energies of the alpha R, alpha L, and C7ax regions. After adiabatic relaxation with flexible geometry, the maps with CHARMM and AMBER became very similar; the lowest energies were observed in the C7eq region, the C5 region (phi approximately -150 degrees, psi approximately 150 degrees) and the C7ax region (phi approximately 70 degrees, psi approximately -70 degrees). Breakdown of the energies, after adiabatic relaxation, into electrostatic, nonbonded, and geometric (including torsional) contributions, showed that (1) with fixed geometry, the nonbonded and torsional contribution to the ECEPP and AMBER potentials were very similar, but the electrostatic contributions were markedly different; (2) with flexible geometry, the nonbonded contribution to the CHARMM and AMBER potentials did not vary greatly over the whole map. The phi-psi maps were subjected to three simple comparisons with experiment. (1) The maps were used to predict the characteristic ratio for poly-L-alanine, and the results were compared with experimental findings (D.A. Brant and P.J. Flory, J. Amer. Chem. Soc. 87, 2788-2791, 1965). The agreement with experiment was acceptable for ECEPP, and for CHARMM after adiabatic relaxation, marginal for AMBER after adiabatic relaxation, and unsatisfactory for CHARMM or AMBER without adiabatic relaxation. (2) Deviations of bond angles from their equilibrium values, in energy-minimized conformations, were compared with values deduced from crystals of terminally-blocked amino acids. With both the CHARMM and AMBER potentials using flexible geometry, one or more excessive deviations was observed in the C7ax local minimum.(ABSTRACT TRUNCATED AT 400 WORDS)

Alanine↗
PubMed1987

Conformational effects of substituting amino acids for glutamine-61 on the central transforming region of the P21 proteins.

The low-energy conformations for a series of peptides based on the sequence of the ras P21 protein from position 55 to position 67 have been computed using conformational energy analysis. These sequences differed at position 61 and contained Gln, Pro, Leu, Lys, and Arg at this position. P21 proteins with Gln, Glu, or Pro at this position do not cause cell transformation at normal levels of expression; proteins with substitutions of at least 14 other amino acids at this position (Leu, Lys, and Arg having been found in tumors in place of the normally occurring Gln-61) do cause malignant transformation of cells in culture. We find that the segments of residues 55-67 from the nontransforming proteins (Gln- or Pro-61) adopt a structure that is energetically unfavorable for the same segment with Leu, Lys, or Arg at position 61. The critical feature of this structure is an alpha-helix from residues 62 to 68. Residue 61 (Gln or Pro) adopts an extended conformation. On the other hand, the segment from transforming proteins can adopt two structures, one all alpha-helical from residue 61 to residue 68 and the other a less-regular, higher-energy structure. The segments from the normal protein can adopt the all alpha-helical structure, a finding that can explain the fact that elevated intracellular levels of the normal protein also cause cell transformation. The results of the calculations suggest that specific changes in the structure of this region can account for the oncogenic effect of the proteins in which substitutions occur.

Amino Acid Sequence↗
PubMed1986

Predicted conformations for the immunodominant region of the circumsporozoite protein of the human malaria parasite Plasmodium falciparum.

The circumsporozoite protein of the human malaria parasite Plasmodium falciparum contains multiple tandem repeats of the amino acid sequence Asn-Ala-Asn-Pro. The repeated sequence encompasses the immunodominant region of the protein, and antibodies raised against it are potent inhibitors of invasion and development of sporozoites in cultured hepatocytes. Using a modified build-up procedure, we have explored a large number of possible helical and near-helical conformations of a terminally blocked tetraicosapeptide, consisting of six repeats of the sequence Asn-Ala-Asn-Pro, and conclude that two helical conformations are energetically favored to the exclusion of all others. One of these conformations is longer, thinner, and left-handed and is likely to be adopted in nonpolar environments, while the other is shorter, broader, and right-handed and should be favored in aqueous solutions. We propose that the immunodominant region of the circumsporozoite protein of P. falciparum adopts one of these conformations in vivo.

Amino Acid Sequence↗
PubMed1984

Some species of human leukocyte interferon are glycosylated.

The carbohydrate content of all of the species of human leukocyte interferon (IFN-alpha) which have been derived from patients with chronic myelogeneous leukemia (CML) and purified to homogeneity has now been determined. Amino sugar content was measured by high-performance liquid chromatography and fluorescamine detection of acid hydrolysates of each sample. Two species showed significant amounts of glucosamine. Most of the purified species of leukocyte interferon from a myeloblast cell line were also tested, and two species were found to contain sugar residues. These forms also differed from the CML interferons in that they revealed the presence of greater amounts of galactosamine. The apparent lack of carbohydrate in some of the higher-molecular-weight species of interferon implicated factors other than glycosylation in the molecular weight differences. The results indicate that some species of IFN-alpha are glycosylated to various degrees.

Amino Sugars↗
PubMed1983

Is adrenal proenkephalin glycosylated?

Adrenal proenkephalin contains the sequence -Asn-Ser-Ser- that is a typical site for the attachment of asparagine-linked carbohydrate. The 5300- and 18,200-Da bovine adrenal proteins derived from proenkephalin contain this recognition sequence and were therefore analyzed for the presence of both amino and neutral sugars. Les than 0.05 mol of amino sugar and less than 0.1 mol of neutral sugar were found per mole of each protein. No amino sugar was detected in other high-molecular-weight adrenal [Met]enkephalin-containing proteins. Together these findings indicate that bovine adrenal proenkephalin does not contain asparagine-linked carbohydrate.

Adrenal Glands↗
PubMed1982

Development of the biochemical and morphological changes induced by administration of a beta-xyloside to chick embryos.

4-Methylumbelliferyl beta-D-xyloside was administered to 9-day-old chick embryos, and the morphological and chemical changes in the embryo were followed daily. Increases in wet weight, Na and Cl content, and visible edema were detectable at 10 days and fully apparent at 11 days. Dry weight increased to the same extent in control and treated embryos for four days, but then diverged. The degree of sulfation of chondroitin sulfate was slightly less in treated than control embryos at 10 days, and reached a steady low value at 11 days. Analysis of glycosaminoglycans in skin, muscle, and aorta showed an increase in chondroitin and its sulfates in the two former tissues but not the latter. In muscle and aorta, the degree of sulfation of chondroitin sulfate was markedly reduced; but in skin the results suggested a more complex picture in which the normal metabolism of glycosaminoglycans was altered. A possible physiological role is suggested for chondroitin sulfate in embryonic soft tissues.

Abnormalities, Drug-Induced↗
PubMed1982

Fluid and glycosaminoglycan excretion by chick embryos treated with a beta-D-xyloside.

Wet weights and glycosaminoglycan content were determined for embryo, amnion, and allantois of control chick embryos and embryos injected with 4-methylumbelliferyl beta-D-xyloside at nine days of age. There was an immediate increase in total uronic acid content, but not in uronic acid concentration, in the embryo. No difference could be detected either in fluid volume, nor in content or type of glycosaminoglycan, in the amnion of the two groups. The fluid content of the allantois fo control eggs increased steadily between nine and 14 days, but in treated embryos the fluid content of the allantois remained low for at least a week. Less than 2 mg of uronic acid was present in allantoic fluid of control 16-day-old embryos, while treated embryos had accumulated more than 8 mg. More than 95% of the latter uronic acid was accounted for as chondroitin sulfate linked to methylumbelliferone and with a degree of sulfation of 50-60%. Thus beta-xyloside-treated embryos excrete large amounts of chondroitin sulfate and very little fluid.

Allantois↗
PubMed1981

Isolation and characterization of the cyanogen bromide peptides derived from the human alpha 2(V) collagen chain.

The human alpha 2(V) collagen chain when cleaved with cyanogen bromide yields ten peptides which can be recovered in approximately equimolar quantities. Characterization of the purified peptides with regard to molecular weight and amino acid composition establishes the uniqueness of the peptides and reveals that the alpha 2(V) chain recovered following limited pepsin digestion contain 956 amino acid residues. Possible homologies between the alpha 2(V) peptides and peptides derived from other collagen chains were noted. In addition, a high-performance liquid chromatography system is described for the separation of three of the alpha 2(V) chain peptides which were not resolved by using conventional separation techniques.

Amino Acids↗
PubMed1979

Changes in chemical composition of chick embryos treated with a beta-xyloside and a lathyrogen.

Nine-day chick embryos were treated with 4-methylumbelliferyl beta-D-xyloside or beta-aminopropionitrile fumarate, and their gross chemical composition was examined one week later. Total DNA was 10--20% less in embryos treated with either drug than it was in control embryos. Xyloside-treated embryos showed marked increases in percent wet weight and in sodium/DNA and chloride/DNA ratios, and small decreases in protein/DNA, hydroxyproline/DNA and sulfate/DNA. None of these parameters was affected in embryos treated with beta-aminopropionitrile. Approximately 85% of the uronic acid of control embryos was present as chondroitin sulfate, with a degree of sulfation of 80% and charge density of 1.8; all of this chondroitin sulfate was covalently linked to peptide and had a number-average molecular weight of 29,300. In embryos treated with beta-xyloside, 90% of the uronic acid was present as chondroitin sulfate, with a degree of sulfation of 40% and charge density ranging from 1 to 2; 27% of this chondroitin sulfate, with an average molecular weight of 25,400, was peptide linked, while 73% was linked to 4-methylumbelliferone and had an average molecular weight of 22,900. The chemical differences between embryos treated with the xyloside and embryos treated with the lathyrogen reinforce the conclusion on morphological grounds that these are distinct syndromes involving different aspects of the extracellular matrix.

Abnormalities, Drug-Induced↗
PubMed1979

Changes in collagen ultrastructure, macroscopic properties and chemical composition of chick embryo cartilage induced by administration of beta-D-xyloside.

Nine-day chick embryos were injected with a beta-xyloside and their sternal cartilage was examined 3 days and a week later. Sterna from 16-day embryos showed a reduction in size as compared to controls, with little or no change in the fraction of extracellular space, and a significant decrease in tensile strength. At the ultrastructural level, collagen fibrils in control sterna were dispersed evenly in the interstitial space, with few contacts between adjacent fibrils. In sterna from treated embryos, almost all collagen fibrils were aggregated into clumps and arrays throughout the interstitial space, with fibril-free areas in between. No abnormalities could be detected in the morphology of individual fibrils or in the ultrastructure of the chondrocytes. The changes in spatial distribution of collagen were fully evident 3 days after drug administration. The hydroxyproline/DNA ratio was the same in control and treated sterna, and no change was observed in the type of collagen. The uronic acid/DNA ratio was reduced by 14% 3 days after drug administration and by 40% after a week. The degree of sulfation of chondroitin sulfate was reduced from 80% in control sterna to 40% in treated sterna; almost all of this chondroitin sulfate was attached to peptide and the sedimentation pattern of the proteoglycan resembled that of normal cartilage proteoglycan. The function of chondroitin sulfate in embryonic cartilage is discussed in terms of our results and others. It is suggested that a major physiological role of the proteoglycan is to control the spatial distribution of collagen fibrils as they assemble to form a cross-linked gel.

Animals↗
PubMed1977

The mode of action of 4-methylumbelliferyl beta-D-xyloside on the synthesis of chondroitin sulphate in embryonic-chicken sternum.

1. Embryonic-chicken sterna, incubated in medium containing 0.1mm-4-methylumbelliferyl beta-d-xyloside (4-methylcoumarin 7-beta-d-xyloside), synthesize proteochondroitin sulphate that is significantly undersulphated and shorter than usual [Gibson, Segen & Audhya (1977) Biochem. J.162, 217-233]. 2. Neither the beta-d-galactoside nor the beta-d-glucuronide of 4-methylumbelliferone, nor 4-methylumbelliferone itself, produced the effects. The only metabolites of 4-methylumbelliferone that were detected in cartilages exposed to 4-methylumbelliferyl beta-d-xyloside were unchanged xyloside and chondroitin sulphate covalently attached to 4-methylumbelliferone. 3. Gel filtration of salt extracts of sterna incubated in medium containing the xyloside showed that there were two pools of chondroitin sulphate in the tissue. One pool was identified, on the basis of its elution pattern and the linear kinetics of incorporation of sulphate into it, as proteochondroitin sulphate. Incorporation into the other pool, whose properties suggested that it was methylumbelliferyl-chondroitin sulphate, indicated that it underwent partial turnover. The molecular weight of this chondroitin sulphate was about 19000, and it appeared to be about 70% sulphated. 4. When sterna were incubated in medium containing the xyloside, there was a very large incorporation of sulphate and glucose into glycosaminoglycans that were released into the incubation medium. This contrasts with incubations of sterna in the absence of the xyloside, in which less than 5% of the sulphate incorporated could be recovered from the medium. The glycosaminoglycan released into the medium was 4-methylumbelliferyl-chondroitin sulphate, whose average molecular weight was 7000-8000 and degree of sulphation more than 95%. 5. Incorporation of sulphate into proteochondroitin sulphate was stimulated more than 3-fold by addition of 20% (v/v) human serum and 10nm-l-3,3',5-tri-iodothyronine. Incorporation into methylumbelliferyl-chondroitin sulphate, in either the tissue or the medium, was not significantly altered. 6. The decrease in chain length and degree of sulphation of proteochondroitin sulphate is explained in terms of competition between peptide-linked primers and methylumbelliferone-containing primers at the intracellular sites of polysaccharidechain elongation and sulphation. The implications of the results for the mechanism of stimulation of proteoglycan synthesis by serum factors are discussed.

Animals↗