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  • 1
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    Effects of natural gas pipeline condensate and crude oil spills, and comments on remediation, with emphasis on south Louisiana salt marshes: a review (2021)
    Louisiana Universities Marine Consortium | Chauvin, LA
    In:  http://aquaticcommons.org/id/eprint/16531 | 30 | 2015-03-30 17:02:26 | 16531 | Louisiana Universities Marine Consortium (LUMCON)
    Details
    Publication Date: 2021-07-06
    Description: This report reviews some of the natural ecological processes at work within a salt marsh as they relate to a spill of natural gas condensate - a mixture of aliphatic hydrocarbons, n-hexane, benzene, toluene, and xylene. It also reviews the environmental impacts of some of the components of natural gas condensate as well as related compounds (crude oil, higher molecular weight hydrocarbons, polycyclic aromatic hydrocarons - PAHs, linear alkyl-benzenes - LABs, etc.) on salt marsh ecosystems in southern Louisiana and elsewhere in the world. The behavior and persistence of these compounds once they have entered the environment is also considered.
    Description: A report to El Paso Energy, Inc., Houston, Texas. PDF includes front matter, 62 pages of text, 40 figures, and 9 tables.
    Keywords: Chemistry ; Ecology ; Environment ; Pollution
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Format: 122
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  • 2
    Electronic Resource
    Electronic Resource
    Correlation of structure with transforming activity of the P21 proteins with substitutions at positions 12 and 16 (1987)
    Springer
    The protein journal 6 (1987), S. 375-385 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; three-dimensional structure ; amino acid substitutions ; P21 proteins ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The structural effects of amino acid substitutions at positions 12 and 16 in the amino-terminal segment (Tyr 4-Ala 18) of the ras-oncogene-encoded P21 proteins have been investigated using conformational energy analysis. The P21 protein with Val at position 12 and Lys at position 16 is known to have high transforming ability, while the P21 protein with Val at position 12 and Asn at position 16 is known to have poor transforming ability, similar to that of the normal protein (with Gly at 12 and Lys at 16.) The current results demonstrate a significant conformational change at position 15 induced by the substitution of Asn for Lys at position 16, which could explain this alteration in transformation potential. These findings are consistent with previous results suggesting the existence of a normal and a malignancy-causing conformation for the P21 proteins and suggest that the critical transforming region may encompass residues 12–15.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02343336
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  • 3
    Electronic Resource
    Electronic Resource
    Structural effects of amino acid substitutions on the matrix protein of vesicular stomatitis virus (1987)
    Springer
    The protein journal 6 (1987), S. 463-472 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; three-dimensional structure ; amino acid substitutions ; matrix protein ; vesicular stomatitis virus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The structural effects of amino acid substitutions for Gly at position 21 in the amino-terminal segment (Lys 15-Pro 26) of the matrix (M) protein of vesicular stomatitis virus (VSV) have been investigated using conformational energy analysis. Monoclonal antibody-binding experiments and protein digestion studies of the M protein indicate that this segment is important to its ribonucleoprotein recognition and its transcription-inhibitory activity. Temperaturesensitive mutants of VSV that do not bind monoclonal antibody and that are devoid of transcription-inhibitory activity are known to have the substitution of Glu for Gly at position 21. The current findings demonstrate a significant conformational change at position 21 induced by the substitution of Glu for Gly, which could explain this alteration in antibody binding and transcription-inhibitory activity. Furthermore, the results indicate that the substitution of any noncyclic L-amino acid for Gly at position 21 may be expected to produce similar changes in M protein function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00276732
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  • 4
    Electronic Resource
    Electronic Resource
    An activating amino acid substitution in the c-abl oncogene protein fails to produce a local conformational change (1991)
    Springer
    The protein journal 10 (1991), S. 437-441 
    Details
    ISSN: 1573-4943
    Keywords: Conformational energy ; three-dimensional structure ; amino acid substitution ; c-abl oncogene ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Thebcr-abl chimeric gene of Philadelphia chromosome positive chronic myelogenous leukemias is only weakly transforming. This transformation activity is greatly enhanced by a Lys-for-Glu substitution at position 832 in the c-abl gene, as occurs in the highly transforming v-abl genes. It has been suggested that this mutation results in a significant structural change in the encoded protein product. Using conformational energy analysis, we have determined the allowed low-energy conformations for residues 828–836 of this protein with Lys and Glu at position 832. In both cases, the overwhelmingly preferred conformation for this region is a bend-helix motif. The helix terminates at residue 836, and there are no discernible differences in conformation between the Lys- and Glu-containing sequences. These results suggest that the activating amino acid substitution at position 832 in the c-abl protein product does not produce its effect via a local conformational change.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01025258
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  • 5
    Electronic Resource
    Electronic Resource
    Correlation of structure with transforming activity of the P21 proteins with substitutions of L-amino acids for Gly at position 13 (1985)
    Springer
    The protein journal 4 (1985), S. 345-352 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; three-dimensional structure ; amino acid substitution ; P21 proteins ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The effects of amino acid substitutions for Gly 13 on the structure of the transforming region (Leu 6-Gly 15) of the P21 proteins have been explored using conformational energy calculations. It has been found that the substitution of Asp for Gly at this position results in a protein capable of transforming cells into malignant ones. Proteins that contain Ser at position 13 (but no other substitutions), however, transform cells with a greatly reduced activity. The transforming peptide with Asp 13 adopts a conformation that is different from the one for the peptide from the normal protein (with Gly 12 and Gly 13) and that may result in expression of a higher energy malignancy-producing form. The Ser-containing peptide adopts as its lowest energy conformation one that is identical to that of the peptide from the normal protein, thus explaining its lack of transforming activity. From analysis of the interactions preventing the Asp 13-containing peptide from adopting the “normal” conformation, it is predicted that substitutions of amino acids with branched side chains atC β, such as Val, Ile, and Thr, should promote cell transformation. This prediction with Val has recently been confirmed in genetic experiments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01025175
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  • 6
    Electronic Resource
    Electronic Resource
    Conformation of the metastasis-inhibiting laminin pentapeptide (1989)
    Springer
    The protein journal 8 (1989), S. 149-157 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; three-dimensional structure ; amino acid substitution ; laminin pentapeptide ; metastasis inhibition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The binding of cancer cells to the basement membrane glycoprotein laminin appears to be a critical step in the metastatic process. This binding can be inhibited competitively by a specific pentapeptide sequence (Tyr-Ile-Gly-Ser-Arg) of the laminin B1 chain, and this peptide can prevent metastasis formationin vivo. However, other similar pentapeptide sequences (e.g., Tyr-Ile-Gly-Ser-Glu) have been found to be much less active in metastasis inhibition, raising the possibility that such amino acid substitutions produce structural changes responsible for altering binding to the laminin receptor. In this study, conformational energy analysis has been used to determine the three-dimensional structures of these peptides. The results indicate that the substitution of Glu for the terminal Arg produces a significant conformational change in the peptide backbone at the middle Gly residue. These results have important implications for the design of drugs that may be useful in preventing metastasis formation and tumor spread.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01025085
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  • 7
    Electronic Resource
    Electronic Resource
    Conformational effects of amino acid substitutions in the P-glycoprotein of themdr 1 gene (1989)
    Springer
    The protein journal 8 (1989), S. 563-573 
    Details
    ISSN: 1573-4943
    Keywords: multidrug resistance ; mutation ; conformational energy analysis ; three-dimensional structure ; structure-function relationships
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The P-glycoprotein of themdr 1 gene is responsible for the phenomenon of multidrug resistance in human cells. The presumed drug-binding site of the wild-type P-glycoprotein contains a glycine at position 185. A mutant P-glycoprotein which contains valine at this position causes cells to retain resistance to colchichine, but to lose cross-resistance to other drugs such as the chemotherapeutic agents vinblastine and Adriamycin. This has been hypothesized to be due to a conformational change in the protein induced by the amino acid substitution. Using conformational energy analysis, we have determined the allowed three-dimensional structures for the wild-type and mutant proteins in the region of position 185. The results indicate that the wild-type protein adopts a unique left-handed conformation at position 185 which is energetically unfavorable for the protein withl-amino acids (including valine) at this position. This conformational change induced by amino acid substitutions for Gly 185 could explain the differences in binding to the P-glycoprotein of various drugs and, hence, the differences in drug resistance exhibited by various cell lines expressing these proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01026439
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  • 8
    Electronic Resource
    Electronic Resource
    Structural effects of amino acid substitutions on the P21 proteins: Evidence for a malignant conformation (1985)
    Springer
    The protein journal 4 (1985), S. 353-362 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; three-dimensional structure ; amino acid substitution ; P21 proteins ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The conformational effects of different amino acid substitutions for Gly at position 12 in theras-oncogene-encoded P21 proteins have been investigated using conformational energy calculations. Mutations that cause amino acid substitutions for Gly 12 result in a protein that produces malignant transformation of cells. It had previously been shown that substitution of Val, Lys, or Ser for Gly at position 12 results in a major conformational change, and that the preferred lowest energy structure for each of the substituted peptides is identical. It is now found that substitution for Gly 12 of other amino acids that have widely disparate helix-nucleating potentials and completely different side chains (Asp, Asn, Cys, Phe, Tle, Leu, and Ala) all produce this identical lowest energy conformation. This finding is consistent with the recent results of site-specific mutagenesis experiments showing that P21 proteins containing these amino acids at position 12 all promote malignant transformation of cells and suggests the existence of a “malignancy-causing” conformation for the P21 proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01025176
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  • 9
    Electronic Resource
    Electronic Resource
    Conformational changes induced by the transforming amino acid substitution in the transmembrane domain of theneu oncogene-encoded p185 protein (1989)
    Springer
    The protein journal 8 (1989), S. 749-756 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; three-dimensional structure ; amino acid substitution ; neu oncogene ; p185 protein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Theneu oncogene is frequently found in certain types of human carcinomas and has been shown to be activated in animal models by nitrosourea-induced mutation. The activating mutation in theneu oncogene results in the substitution of a glutamic acid for a valine at position 664 in the transmembrane domain of the encoded protein product of 185 kda (designated p185), which, on the basis of homology studies, is presumed to be a receptor for an as yet unidentified growth factor. It has been proposed that activating amino acid substitutions in this region of p185 lead to a conformational change in the protein which causes signal transduction via an increase in tyrosine kinase activity in the absence of any external signal. Using conformational energy analysis, we have determined the preferred three-dimensional structures for the transmembrane decapeptide (residues 658–667) of the p185 protein with valine and glutamic acid at the critical position 664. The results indicate that the global minimum energy conformation of the decapeptide from the normal protein with Val at position 664 is an α-helix with a sharp bend (CD* conformation at residues 664 and 665) in this region, whereas the global minimum conformation for the decapeptide from the mutant transforming protein with Glu at position 664 assumes an all α-helical configuration. Furthermore, the second highest energy conformation for the decapeptide from the normal protein is identical to the global minimum energy conformation for the decapeptide from the transforming protein, providing a possible explanation why overexpression of the normal protein also has a transforming effect. These results suggest there may be a normal and a transforming conformation for theneu-encoded p185 proteins which may explain their differences in transforming activity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01024899
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  • 10
    Electronic Resource
    Electronic Resource
    Conformational energy analysis of the leucine repeat regions of C/EBP, GCN4, and the proteins of themyc, jun, andfos oncogenes (1989)
    Springer
    The protein journal 8 (1989), S. 679-688 
    Details
    ISSN: 1573-4943
    Keywords: amphipathic helix ; leucine zipper ; DNA binding proteins ; conformational energy analysis ; three-dimensional structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract It has been recently proposed that certain DNA binding proteins (including C/EBP, GCN4 and themyc, jun, andfos oncogene proteins) share a common structural motif based on helix-promoting regions containing heptad repeat sequences of leucines. It has been suggested that this structure is critical to the biological activity of these proteins, since it facilitates the formation of functional dimers held together by interdigitating leucine side-chains along the hydrophobic interfaces between long α-helical regions of the polypeptide chains in a configuration termed the “leucine zipper.” In this paper, conformational energy analysis is used to determine the preferred three-dimensional structures of the leucine repeat regions of these proteins. The results indicate that, in all cases, the global minimum energy conformation for these regions is an amphipathic α-helix with the leucine side-chains arrayed on one side in such a way to favor “leucine zipper” dimerization. Furthermore, amino acid substitutions in these regions (such as Pro for Leu), that are known to inhibit dimer formation and prevent DNA binding, are found to produce significant conformational changes that disrupt the amphipathic helical structure. Thus, these results provide support for the proposed “leucine zipper” configuration as a critical structural feature of this class of DNA binding proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01025608
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