Primary Citation PubMed: 9302995
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Refinement and prediction of protein prenylation motifs.
(2005) Genome Biol 6
PubMed: 15960807 | PubMedCentral: PMC1175975 | DOI: 10.1186/gb-2005-6-6-r55
Indeed, in several resolved structures of in vivo prenylated GTPases, secondary structural elements such as helices that stabilize the fold of the protein are typically found only at the amino-termina... side of that linker region (beginning of helix at positions -12 (PDB identifier 1FTN), -13 (PDB 1MH1), -15 (PDB 1AM4), -12 (PDB 1A4R)).
Publication Year: 2005
Structure-based predictive models for allosteric hot spots.
(2009) PLoS Comput Biol 5
PubMed: 19816556 | PubMedCentral: PMC2748687 | DOI: 10.1371/journal.pcbi.1000531
PDB of effector ligand-unbound (inactive state) PDB of effector ligand-bound (active state) Training Data Set Proteins CheY (signal transduction) 3chy 1fqw PurR repressor (transcription factor) 1dbq 1... et Tet repressor (transcription factor) 2trt 1qpi Hemoglobin (carrier protein/enzyme) 4hhb 1hho Phosphofructokinase (enzyme) 6pfk 4pfk phosphoglycerate dehydrogenase (enzyme) 1psd 1yba fructose-1,6-bisphosphatase (enzyme) 1eyj 1eyi Aspartate transcarbamoylase (enzyme) 1rac 1d09 RhoA (signal transduction) 1ftn 1a2b CDC-42 (signal transduction) 1an0 1nf3 glycogen phosphorylase (transcription factor) 1gpb 7gpb Independent Data Set Proteins glucokinase (enzyme) 1v4t 1v4s glutamate dehydrogenase (enzyme) 1nr7 1hwz lac repressor (transcription factor) 1tlf 1efa myosin II (motor protein/enzyme) 1vom 1fmw thrombin (enzyme) 1sgi 1sg8 Since the Michaelis constant, K M , has been shown to be an apparent dissociation constant, taking into account all substrate-bound species of enzyme, and is directly proportional to K S , we may replace K S with K M in (2)  .
Publication Year: 2009
Nucleotide binding switches the information flow in ras GTPases.
(2011) PLoS Comput Biol 7
PubMed: 21390270 | PubMedCentral: PMC3048383 | DOI: 10.1371/journal.pcbi.1001098
Methods Simulated proteins The following S GDP and S GTP representatives of the Arf1, Gα t , Sec4, H-Ras, and RhoA families were selected as input of MD simulations: Arf1 (PDB codes: 1HUR and ... O3Y), Gα t (PDB codes: 1TAG and 1TND), Sec4 (PDB codes: 1G16 and 1G17), H-Ras (PDB codes: 4Q21 and 5Q21), and RhoA (PDB codes: 1FTN and 1KMQ) based on the following criteria: i) homogeneity of the molecular specie, i.e. same sequence, for the two functional states, and ii) existence of a crystal structure for the isolated state, i.e. not in complex with other proteins.
Publication Year: 2011
Computing the protein binding sites.
(2012) BMC Bioinformatics 13 Suppl 10
PubMed: 22759425 | PubMedCentral: PMC3382440 | DOI: 10.1186/1471-2105-13-S10-S2
G proteins family in P-loop folds We select 5 proteins (1A2B, 1CXZ, 1DPF, 1FTN, 1S1C) from G proteins family in P-loop folds.
Publication Year: 2012
Identification of potential small molecule binding pockets on Rho family GTPases.
(2012) PLoS One 7
PubMed: 22815826 | PubMedCentral: PMC3397943 | DOI: 10.1371/journal.pone.0040809
Both the secondary structure and residue numbering are according to the RhoA-GDP complex from Homo Sapiens (PDB code 1FTN).
(B) The molecular structure of representative the GTP and GDP-bound Rho conformations (PDB codes: 1KMQ and 1FTN).
The protein structure of reference corresponds to the RhoA-GDP complex from Homo Sapiens (PDB code 1FTN).
Fragment probe occupancy per position in a single crystal structure (PDB code 1FTN, gray bars) and averaged across all available crystal structures (black lines, see main text for details).
We first carried out three 30 ns long cMD simulations, commencing from each of the three major conformational states (PDB codes for the initial structure models are 1A2B, 1FTN and 1LB1 for the GTP GDP and APO states respectively, see Figure 2 ).
Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition.
PubMed: 22844485 | PubMedCentral: PMC3402401 | DOI: 10.1371/journal.pone.0041518
Consequently the structure of RhoA bound to GDP was chosen (PDBID: 1FTN) for macromolecular docking  .
PubMed ID is not available.
Published in 2015
( c ) Superposition of the effector loops of GlcNAcylated RhoA with structures of non-glycosylated active GTPγS-bound RhoA (pdb code 1A2B) 42 and inactive GDP-bound RhoA (pdb code 1FTN) 41 .
Publication Year: 2015
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