[1]
|
K. Wennerberg, K. L. Rossman and C. J. Der, “The Ras Superfamily at a Glance,” Journal of Cell Science, Vol. 118, No. 5, 2005, pp. 843-846. doi:10.1242/jcs.01660
|
[2]
|
M. Macaluso, G. Russo, C. Cinti, et al., “Ras Family Genes: An Interesting Link between Cell Cycle and Cancer,” Journal of Cellular Physiology, Vol. 192, No. 2, 2002, pp. 125-130. doi:10.1002/jcp.10109
|
[3]
|
A. Fernández-Medarde and E. Santos, “Ras in Cancer and Developmental Diseases,” Genes & Cancer, Vol. 2, No. 3, 2011, pp. 344-358. doi:10.1177/1947601911411084
|
[4]
|
J. L. Bos, “Ras Oncogenes in Human Cancer: A Review,” Cancer Research, Vol. 49, No. 17, 1989, pp. 4682-4689.
|
[5]
|
C. A. Ellis and G. Clark, “The Importance of Being KRas,” Cellular Signalling, Vol. 12, No. 7, 2000, pp. 425-434. doi:10.1016/S0898-6568(00)00084-X
|
[6]
|
J. W. Keller, J. L. Franklin, R. Graves-Deal, et al., “Oncogenic KRAS Provides a Uniquely Powerful and Variable Oncogenic Contribution among RAS Family Members in the Colonic Epithelium,” Journal of Cellular Physiology, Vol. 210, No. 3, 2007, pp. 740-749. doi:10.1002/jcp.20898
|
[7]
|
I. Macara, K. Lounsbury, S. Richards, et al., “The Ras Superfamily of GTPases,” The FASEB Journal, Vol. 10, No. 5, 1996, pp. 625-630.
|
[8]
|
K. Scheffzek, M. R. Ahmadian, W. Kabsch, et al., “The Ras-RasGAP Complex: Structural Basis for GTPase Activation and Its Loss in Oncogenic Ras Mutants,” Science, Vol. 277, No. 5324, 1997, pp. 333-339.
doi:10.1126/science.277.5324.333
|
[9]
|
C. K?tting, A. Kallenbach, Y. Suveyzdis, et al., “The GAP Arginine Finger Movement into the Catalytic Site of Ras Increases the Activation Entropy,” Proceedings of the National Academy of Sciences, Vol. 105, No. 17, 2008, pp. 6260-6265. doi:10.1073/pnas.0712095105
|
[10]
|
H. te Heesen, K. Gerwert and J. Schlitter, “Role of the Arginine Finger in Ras?RasGAP Revealed by QM/MM Calculations,” FEBS Letters, Vol. 581, No. 29, 2007, pp. 5677-5684. doi:10.1016/j.febslet.2007.11.026
|
[11]
|
B. L. Grigorenko, A. V. Nemukhin, I. A. Topol, et al., “QM/MM Modeling the Ras-GAP Catalyzed Hydrolysis of Guanosine Triphosphate,” Proteins: Structure, Function, and Bioinformatics, Vol. 60, No. 3, 2005, pp. 495-503.
doi:10.1002/prot.20472
|
[12]
|
H. Kiaris and D. A. Spandidos, “Mutations of Ras Genes in Human Tumours (Review),” International Journal of Oncology, Vol. 7, No. 3, 1995, pp. 413-421.
|
[13]
|
P. Wegman, C. Ahlin and B. Sorbe, “Genetic Alterations in the K-Ras Gene Influence the Prognosis in Patients with Cervical Cancer Treated by Radiotherapy,” International Journal of Gynecological Cancer, Vol. 21, No. 1, 2011, pp. 86-91. doi:10.1097/IGC.0b013e3182049924
|
[14]
|
S. R. Lin, C. H. Hsu, J. H. Tsai, et al., “Decreased GTPase Activity of K-Ras Mutants Deriving from Human Functional Adrenocortical Tumours,” British Journal of Cancer, Vol. 82, No. 5, 2000, pp. 1035-1040.
|
[15]
|
M. S. Nur-E-Kamal, A. Sizeland, G. D’Abaco, et al., “Asparagine 26, Glutamic Acid 31, Valine 45, and Tyrosine 64 of Ras Proteins Are Required for Their Oncogenicity,” Journal of Biological Chemistry, Vol. 267, No. 3, 1992, pp. 1415-1418.
|
[16]
|
C. Oliveira, J. L. Westra, D. Arango, et al., “Distinct Patterns of KRAS Mutations in Colorectal Carcinomas According to Germline Mismatch Repair Defects and hMLH1 Methylation Status,” Human Molecular Genetics, Vol. 13, No. 19, 2004, pp. 2303-2311.
doi:10.1093/hmg/ddh238
|
[17]
|
Y. Li, G. Bollag, R. Clark, et al., “Somatic Mutations in the Neurofibromatosis 1 Gene in Human Tumors,” Cell, Vol. 69, No. 2, 1992, pp. 275-28.
doi:10.1016/0092-8674(92)90408-5
|
[18]
|
K. Scheffzek, M. R. Ahmadian, L. Wiesmüller, et al., “Structural Analysis of the GAP-Related Domain from Neurofibromin and Its Implications,” The EMBO Journal, Vol. 17, No. 15, 1998, pp. 4313-4327.
doi:10.1093/emboj/17.15.4313
|
[19]
|
Molecular Operating Enviroment (MOE), Chemical Computing Group: Montreal, 2009.
|
[20]
|
B. Hess, C. Kutzner, D. van der Spoel, et al., “GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation,” Journal of Chemical Theory and Computation, Vol. 4, No. 3, 2008, pp. 435-447. doi:10.1021/ct700301q
|
[21]
|
J. Wang, P. Cieplak and P. A. Kollman, “How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?” Journal of Computational Chemistry, Vol. 21, No. 12, 2000, pp. 1049-1074.
doi:10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F
|
[22]
|
K. L. Meagher, L. T. Redman and H. A. Carlson, “Development of Polyphosphate Parameters for Use with the AMBER Force Field,” Journal of Computational Chemistry, Vol. 24, No. 9, 2003, pp. 1016-1025.
doi:10.1002/jcc.10262
|
[23]
|
U. Essmann, L. Perera, M. Berkowitz, et al., “A Smooth Particle Mesh Ewald Method,” The Journal of Chemical Physics, Vol. 103, No. 19, 1995, pp. 8577-8593.
doi:10.1063/1.470117
|
[24]
|
T. Darden, D. York and L. Pedersen, “Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems,” The Journal of Chemical Physics, Vol. 98, No. 12, 1993, pp. 10089-10092. doi:10.1063/1.464397
|
[25]
|
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, et al., “Molecular Dynamics with Coupling to an External Bath,” The Journal of Chemical Physics, Vol. 81, No. 8, 1984, pp. 3684-3690. doi:10.1063/1.448118
|
[26]
|
B. Hess, H. Bekker, H. J. C. Berendsen, et al., “LINCS: A Linear Constraint Solver for Molecular Simulations,” Journal of Computational Chemistry, Vol. 18, No. 12, 1997, pp. 1463-1472.
doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
|
[27]
|
W. G. Hoover, “Canonical Dynamics: Equilibrium PhaseSpace Distributions,” Physical Review A, Vol. 31, No. 3, 1985, pp. 1695-1697. doi:10.1103/PhysRevA.31.1695
|
[28]
|
M. Parrinello and A. Rahman, “Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method,” Journal of Applied Physics, Vol. 52, No. 12, 1981, pp. 7182-7190. doi:10.1063/1.328693
|
[29]
|
A. A. Gorfe, B. J. Grant and J. A. McCammon, “Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins,” Structure (London, England: 1993), Vol. 16, No. 6, 2008, pp. 885-896.
|
[30]
|
S. Lukman, B. J. Grant, A. A. Gorfe, et al., “The Distinct Conformational Dynamics of K-Ras and H-Ras A59G,” PLoS Computational Biology, Vol. 6, No. 9, 2010, Article ID: e1000922. doi:10.1371/journal.pcbi.1000922
|