Differential dynamics of RAS isoforms in GDP- and GTP-bound states. 2015

Abhijeet Kapoor, and Alex Travesset
Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011.

RAS subfamily proteins regulates cell growth promoting signaling processes by cycling between active (GTP-bound) and inactive (GDP-bound) states. Different RAS isoforms, though structurally similar, exhibit functional specificity and are associated with different types of cancers and developmental disorders. Understanding the dynamical differences between the isoforms is crucial for the design of inhibitors that can selectively target a particular malfunctioning isoform. In this study, we provide a comprehensive comparison of the dynamics of all the three RAS isoforms (HRAS, KRAS, and NRAS) using extensive molecular dynamics simulations in both the GDP- (total of 3.06 μs) and GTP-bound (total of 2.4 μs) states. We observed significant differences in the dynamics of the isoforms, which rather interestingly, varied depending on the type of the nucleotide bound and the simulation temperature. Both SwitchI (Residues 25-40) and SwitchII (Residues 59-75) differ significantly in their flexibility in the three isoforms. Furthermore, Principal Component Analysis showed that there are differences in the conformational space sampled by the GTP-bound RAS isoforms. We also identified a previously unreported pocket, which opens transiently during MD simulations, and can be targeted to regulate nucleotide exchange reaction or possibly interfere with membrane localization. Further, we present the first simulation study showing GDP destabilization in the wild-type RAS protein. The destabilization of GDP/GTP occurred only in 1/50 simulations, emphasizing the need of guanine nucleotide exchange factors (GEFs) to accelerate such an extremely unfavorable process. This observation along with the other results presented in this article further support our previously hypothesized mechanism of GEF-assisted nucleotide exchange.

UI MeSH Term Description Entries
D006153 Guanosine Diphosphate A guanine nucleotide containing two phosphate groups esterified to the sugar moiety. GDP,Guanosine 5'-Diphosphate,Guanosine 5'-Trihydrogen Diphosphate,5'-Diphosphate, Guanosine,5'-Trihydrogen Diphosphate, Guanosine,Diphosphate, Guanosine,Diphosphate, Guanosine 5'-Trihydrogen,Guanosine 5' Diphosphate,Guanosine 5' Trihydrogen Diphosphate
D006160 Guanosine Triphosphate Guanosine 5'-(tetrahydrogen triphosphate). A guanine nucleotide containing three phosphate groups esterified to the sugar moiety. GTP,Triphosphate, Guanosine
D013499 Surface Properties Characteristics or attributes of the outer boundaries of objects, including molecules. Properties, Surface,Property, Surface,Surface Property
D055672 Static Electricity The accumulation of an electric charge on a object Electrostatic,Electrostatics,Static Charge,Charge, Static,Charges, Static,Electricity, Static,Static Charges
D056004 Molecular Dynamics Simulation A computer simulation developed to study the motion of molecules over a period of time. Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics
D018631 ras Proteins Small, monomeric GTP-binding proteins encoded by ras genes (GENES, RAS). The protooncogene-derived protein, PROTO-ONCOGENE PROTEIN P21(RAS), plays a role in normal cellular growth, differentiation and development. The oncogene-derived protein ONCOGENE PROTEIN P21(RAS) can play a role in aberrant cellular regulation during neoplastic cell transformation (CELL TRANSFORMATION, NEOPLASTIC). This enzyme was formerly listed as EC 3.6.1.47. Gene Products, ras,ras GTPase,ras Protein,ras GTPases,GTPase, ras,GTPases, ras,Protein, ras,ras Gene Products
D020033 Protein Isoforms Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING. Isoform,Isoforms,Protein Isoform,Protein Splice Variant,Splice Variants, Protein,Protein Splice Variants,Isoform, Protein,Isoforms, Protein,Splice Variant, Protein,Variant, Protein Splice,Variants, Protein Splice

Related Publications

Abhijeet Kapoor, and Alex Travesset
April 1997, Protein engineering,
Abhijeet Kapoor, and Alex Travesset
December 2009, Biochemistry,
Abhijeet Kapoor, and Alex Travesset
April 2018, International journal of molecular sciences,
Abhijeet Kapoor, and Alex Travesset
April 2001, Biochemistry,
Abhijeet Kapoor, and Alex Travesset
December 2017, Cell chemical biology,
Abhijeet Kapoor, and Alex Travesset
February 2004, Journal of biochemical and biophysical methods,
Abhijeet Kapoor, and Alex Travesset
February 2014, Biological chemistry,
Abhijeet Kapoor, and Alex Travesset
July 2010, The Journal of biological chemistry,
Copied contents to your clipboard!