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  • 1
    Electronic Resource
    Electronic Resource
    Conformational effects of the substitution of ARG for GLY 13 in theras oncogene-encoded P21 protein (1988)
    Springer
    The protein journal 7 (1988), S. 349-354 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; amino acid substitution ; position 13 ; P21 protein ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The effect of the substitution of Arg for Gly 13 on the structure of the transforming region decapeptide (Leu 6-Gly 15) of the ras oncogene encoded P21 protein has been investigated using conformational energy analysis. A human malignancy has been identified that contains a ras gene with a single mutation in the thirteenth codon such that the encoded protein would have Arg substituted for Gly at this position, and transfection of cells in culture with this gene results in malignant transformation. Conformational analysis demonstrates that the Arg 13 decapeptide adopts a conformation identical to that for other peptides with substitutions at position 13 (Asp 13, Val 13) from transforming proteins that is distinctively different from that for peptides (Gly 13, Ser 13) from normal, nontransforming proteins. This is found to be an indirect effect resulting from changes in the conformation of Gly 12 produced by substitutions at position 13. These results are consistent with recent analysis of crystallographic data of proteins on conformational preferences for glycine in tripeptide sequences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01024884
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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
    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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  • 5
    Electronic Resource
    Electronic Resource
    Conformational effects of amino acid substitutions at positions 10, 12, and 13 in the P21 protein (1989)
    Springer
    The protein journal 8 (1989), S. 79-86 
    Details
    ISSN: 1573-4943
    Keywords: conformational energy ; amino acid substitution ; P21 protein ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Substitutions of amino acids for Gly 12 or Gly 13 in theras oncogene-encoded P21 proteins have been demonstrated to produce unique structural changes in these proteins that correlate with their ability to produce cell transformation. For example, the P21 proteins with Arg 12 or Val 13 are both known to be actively transforming. Recent site-specific mutagenesis experiments on the transforming Arg 12 protein have found that the substitution of Val for Gly 10 has no effect on transforming activity whereas the substitution of Val for Gly 13 led to a loss of transforming activity. In this study, we examine the structural effects of these substitutions on the amino terminal hydrophobic decapeptide (Leu 6-Gly 15) of P21 using conformational energy analysis. The results show that the transforming proteins with Gly 10 and Arg 12 or Val 10 and Arg 12 can both adopt the putative malignancy-causing conformation, whereas, for the nontransforming protein with Arg 12 and Val 13, this conformation is energetically disallowed. These results further support the theory that due to structural changes the transforming P21 proteins are unable to bind to some regulatory cellular element which may be the recently identified binding protein responsible for the induction of increased GTPase activity in normal P21 compared with transforming mutants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01025080
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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
    Comparison of the predicted structure for the activated form of the P21 protein with the X-ray crystal structure (1990)
    Springer
    The protein journal 9 (1990), S. 543-547 
    Details
    ISSN: 1573-4943
    Keywords: Predicted structure ; activated form ; p21 protein ; conformational energy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The predicted conformation and position of the central transforming region (residues 55–67) of the p21 protein are compared with the conformation and position of this segment in a recently determined X-ray crystal structure of residues 1–166 of this protein in the activated state bound to a nonhydrolyzable GTP derivative. We previously predicted that this segment of the protein would adopt a roughly extended conformation from Ile 55-Thr 58, a reverse turn at Ala 59-Gln 61, followed by an α-helix from Glu 62-Met 67. We further predicted that this region of the activated protein occupies a position that is virtually identical to corresponding regions in the homologous purine nucleotide-binding proteins, bacterial elongation factor (EF-tu), and adenylate kinase (ADK). We find that there is a close correspondence between the conformation and position of our predicted structure and those found in the X-ray crystal structure. A mechanism for activation of the protein is proposed and is corroborated by X-ray crystallographic data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01025007
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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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